Multiple platform build/check report for BioC 3.17 - CHECK results for affy on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)	x86_64	4.3.0 alpha (2023-04-03 r84154)	4547
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"	4333
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings affy_1.77.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/affy.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.77.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘affy’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Things done:
      0 (wh:) moved everything related to Cdf-class from 'affy' to 'makecdfenv':
        R/Cdf.R, R/getLocationsData.Cdf.R, locate.name.R, pmormm.R
        R/read.cdffile.R, data/cdf.example.rda, man/Cdf-class.Rd
        man/getLocationsData.Cdf.Rd, man/locate.name.Rd, man/pmormm.Rd
        man/read.cdffile.Rd, src/read_cdffile.c
      o read.affybatch2 reads all cel files together in one big hit
        into an affybatch
      o the baseline in normalize.AffyBatch,invariant can be selected
        using a baseline.type parameter. Also changed "progress" to the 
        more standard "verbose". Seemed to be an error since both PM and
        MM probes were normalized by only PM's where used to establish the 
        normalization, now follows same standard as been introduced for
        normalize.AffyBatch.quantiles.
      o Most normalization routines can now be called with the parameter 
        type which specifies whether to be pmonly, mmonly, both together 
        or both separately. This introduces more consistency to the how
        the normalization routines are actually applied to affybatchs.
      o express() has been completely removed.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘stats:::C_loess_raw’ ‘stats:::C_lowesp’ ‘stats:::C_lowesw’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls to a base package:
  .C(stats:::C_loess_raw, ...)
  .Fortran(stats:::C_lowesp, ...)
  .Fortran(stats:::C_lowesw, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (7) normalize.quantiles.Rd:40: Invalid email address: bmbolstad.com
checkRd: (-1) xy2indices.Rd:51: Escaped LaTeX specials: \_ \_
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘affy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AffyBatch-class
> ### Title: Class AffyBatch
> ### Aliases: AffyBatch-class AffyBatch,ANY AffyBatch probes geneNames
> ###   geneNames<- getCdfInfo image indexProbes intensity<- intensity
> ###   pmindex mmindex probeset $.AffyBatch cdfName cdfName,AffyBatch-method
> ###   checkValidFilenames probes,AffyBatch-method exprs,AffyBatch-method
> ###   exprs<-,AffyBatch,ANY-method se.exprs,AffyBatch-method
> ###   se.exprs<-,AffyBatch-method featureNames,AffyBatch-method
> ###   featureNames<-,AffyBatch-method geneNames,AffyBatch-method
> ###   geneNames<-,AffyBatch,ANY-method getCdfInfo,AffyBatch-method
> ###   image,AffyBatch-method initialize,AffyBatch-method
> ###   indexProbes,AffyBatch-method intensity<-,AffyBatch-method
> ###   intensity,AffyBatch-method pmindex,AffyBatch-method
> ###   mmindex,AffyBatch-method probeset,AffyBatch-method
> ###   boxplot,AffyBatch-method dim,AffyBatch-method row,AffyBatch-method
> ###   col,AffyBatch-method show,AffyBatch-method pm,AffyBatch-method
> ###   pm<-,AffyBatch,ANY-method mm,AffyBatch-method
> ###   mm<-,AffyBatch,ANY-method probeNames,AffyBatch-method
> ###   hist,AffyBatch-method [<-,AffyBatch-method [,AffyBatch-method
> ###   [[,AffyBatch-method length,AffyBatch-method
> ###   bg.correct,AffyBatch,character-method
> ###   indexProbes,AffyBatch,character-method
> ###   indexProbes,AffyBatch,missing-method
> ###   computeExprSet,AffyBatch,character,character-method
> ###   cdfName,AffyBatch-method updateObject,AffyBatch-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   ## load example
+   data(Dilution)
+ 
+   ## nice print
+   print(Dilution)
+ 
+   pm(Dilution)[1:5,]
+   mm(Dilution)[1:5,]
+ 
+   ## get indexes for the PM probes for the affyID "1900_at" 
+   mypmindex <- pmindex(Dilution,"1900_at")
+   ## same operation using the primitive
+   mypmindex <- indexProbes(Dilution, which="pm", genenames="1900_at")[[1]]
+   ## get the probe intensities from the index
+   intensity(Dilution)[mypmindex, ]
+ 
+   description(Dilution) ##we can also use the methods of eSet
+   sampleNames(Dilution)
+   abstract(Dilution)
+ }
Loading required package: affydata
     Package    LibPath                                        Item      
[1,] "affydata" "/home/biocbuild/bbs-3.17-bioc/R/site-library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
also installing the dependencies ‘sys’, ‘bitops’, ‘cli’, ‘glue’, ‘lifecycle’, ‘fastmap’, ‘askpass’, ‘RCurl’, ‘GenomeInfoDbData’, ‘bit’, ‘rlang’, ‘vctrs’, ‘cachem’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘R6’, ‘XVector’, ‘GenomeInfoDb’, ‘crayon’, ‘bit64’, ‘blob’, ‘memoise’, ‘pkgconfig’, ‘httr’, ‘png’, ‘Biostrings’, ‘IRanges’, ‘DBI’, ‘RSQLite’, ‘S4Vectors’, ‘KEGGREST’, ‘AnnotationDbi’

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* installing *source* package ‘sys’ ...
** package ‘sys’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c exec.c -o exec.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o sys.so exec.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-sys/00new/sys/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sys)
* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bit-ops.c -o bit-ops.o
bit-ops.c: In function ‘bitShiftL’:
bit-ops.c:125:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  125 |                 else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’
  145 |     bitshift_BODY( << );
      |     ^~~~~~~~~~~~~
bit-ops.c:136:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  136 |                 else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:145:5: note: in expansion of macro ‘bitshift_BODY’
  145 |     bitshift_BODY( << );
      |     ^~~~~~~~~~~~~
bit-ops.c: In function ‘bitShiftR’:
bit-ops.c:125:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  125 |                 else *(xaAb++)=(double) (_2_UINT_(xa[i]) __OP__ I_2_UINT(xb[j] & 31 ) ) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’
  149 |     bitshift_BODY( >> );
      |     ^~~~~~~~~~~~~
bit-ops.c:136:80: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  136 |                 else *(xaAb++)=(double) (_2_UINT_(xa[j]) __OP__ I_2_UINT(xb[i] & 31 )) ; \
      |                                                                                ^
bit-ops.c:6:50: note: in definition of macro ‘I_2_UINT’
    6 | #define I_2_UINT(I)   (unsigned int) ((I) < 0 ? (I + UINT_MAX +1) : (I))
      |                                                  ^
bit-ops.c:149:5: note: in expansion of macro ‘bitshift_BODY’
  149 |     bitshift_BODY( >> );
      |     ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cksum.c -o cksum.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bitops.so bit-ops.o cksum.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-bitops/00new/bitops/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bitops)
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c ansi.c -o ansi.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c cleancall.c -o cleancall.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c diff.c -o diff.o
diff.c: In function ‘clic_diff_chr’:
diff.c:104:3: warning: ‘sn’ may be used uninitialized [-Wmaybe-uninitialized]
  104 |   SET_VECTOR_ELT(result, 0, allocVector(INTSXP, sn));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c errors.c -o errors.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c inst.c -o inst.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress-unix.c -o keypress-unix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress-win.c -o keypress-win.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c keypress.c -o keypress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c md5.c -o md5.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c progress-altrep.c -o progress-altrep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c progress.c -o progress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c sha1.c -o sha1.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c sha256.c -o sha256.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c thread.c -o thread.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c tty.c -o tty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c utf8.c -o utf8.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vt.c -o vt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vtparse.c -o vtparse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c vtparse_table.c -o vtparse_table.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c win-utf8.c -o win-utf8.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fvisibility=hidden -I../inst/include -fpic  -g -O2  -Wall -c winfiles.c -o winfiles.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-cli/00new/cli/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cli)
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c glue.c -o glue.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c trim.c -o trim.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-glue/00new/glue/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (glue)
* installing *source* package ‘fastmap’ ...
** package ‘fastmap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ilib/  -I/usr/local/include   -DR_NO_REMAP -fpic  -g -O2  -Wall -c fastmap.cpp -o fastmap.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ilib/  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o fastmap.so fastmap.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-fastmap/00new/fastmap/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fastmap)
* installing *source* package ‘GenomeInfoDbData’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)
* installing *source* package ‘bit’ ...
** package ‘bit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c attrutil.c -o attrutil.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bit.c -o bit.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c chunkutil.c -o chunkutil.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c clone.c -o clone.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integerutil.c -o integerutil.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c merge.c -o merge.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort.c -o sort.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bit.so attrutil.o bit.o chunkutil.o clone.o init.o integerutil.o merge.o rle.o sort.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-bit/00new/bit/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bit)
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c capture.c -o capture.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c internal.c -o internal.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang/  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o rlang.so capture.o internal.o rlang.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-rlang/00new/rlang/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rlang)
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
Using PKG_LIBS=-lcurl
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c callbacks.c -o callbacks.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c download.c -o download.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c escape.c -o escape.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fetch.c -o fetch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c form.c -o form.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c getdate.c -o getdate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c handle.c -o handle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ieproxy.c -o ieproxy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c interrupt.c -o interrupt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c multi.c -o multi.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c nslookup.c -o nslookup.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c options.c -o options.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c reflist.c -o reflist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typechecking.c -o typechecking.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c winidn.c -o winidn.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -DSTRICT_R_HEADERS  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c writer.c -o writer.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-curl/00new/curl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (curl)
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_array.c -o collapse_array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_object.c -o collapse_object.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c collapse_pretty.c -o collapse_pretty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c escape_chars.c -o escape_chars.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c integer64_to_na.c -o integer64_to_na.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_datelist.c -o is_datelist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_recordlist.c -o is_recordlist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c is_scalarlist.c -o is_scalarlist.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c modp_numtoa.c -o modp_numtoa.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c null_to_na.c -o null_to_na.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c num_to_char.c -o num_to_char.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c parse.c -o parse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c prettify.c -o prettify.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c push_parser.c -o push_parser.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c r-base64.c -o r-base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c register.c -o register.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c row_collapse.c -o row_collapse.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c transpose_list.c -o transpose_list.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c validate.c -o validate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl.c -o yajl/yajl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Iyajl/api  -I/usr/local/include   -fvisibility=hidden  -fpic  -g -O2  -Wall -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-jsonlite/00new/jsonlite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs”
in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime”
in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms”
in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json”
in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64”
in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist”
in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob”
in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar”
in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf”
in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (jsonlite)
* installing *source* package ‘mime’ ...
** package ‘mime’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rawmatch.c -o rawmatch.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o mime.so init.o rawmatch.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-mime/00new/mime/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mime)
* installing *source* package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R6)
* installing *source* package ‘crayon’ ...
** package ‘crayon’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (crayon)
* installing *source* package ‘pkgconfig’ ...
** package ‘pkgconfig’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pkgconfig)
* installing *source* package ‘png’ ...
** package ‘png’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fpic  -g -O2  -Wall -c dummy.c -o dummy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fpic  -g -O2  -Wall -c read.c -o read.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    `libpng-config --cflags` -fpic  -g -O2  -Wall -c write.c -o write.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o png.so dummy.o read.o write.o -lpng16 -lm -lz -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-png/00new/png/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (png)
* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DBI)
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c AEbufs.c -o AEbufs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Hits_class.c -o Hits_class.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
Hits_class.c: In function ‘Hits_new’:
/home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:886:33: warning: ‘revmap’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  886 | #define defineVar               Rf_defineVar
      |                                 ^~~~~~~~~~~~
Hits_class.c:216:19: note: ‘revmap’ was declared here
  216 |         SEXP ans, revmap, symbol;
      |                   ^~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c LLint_class.c -o LLint_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c List_class.c -o List_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Rle_class.c -o Rle_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Rle_utils.c -o Rle_utils.o
Rle_utils.c: In function ‘Rle_real_runq’:
Rle_utils.c:701:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  701 |                                 if (count_na != 0)
      |                                 ^~
Rle_utils.c:703:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  703 |                                         q_index = roundingScale(window_len_na,
      |                                         ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c character_utils.c -o character_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c eval_utils.c -o eval_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c hash_utils.c -o hash_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integer_utils.c -o integer_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c logical_utils.c -o logical_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c raw_utils.c -o raw_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c safe_arithm.c -o safe_arithm.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function]
  263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc)
      |             ^~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c vector_utils.c -o vector_utils.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-S4Vectors/00new/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List”
Creating a new generic function for ‘unname’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame”
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table”
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (S4Vectors)
* installing *source* package ‘lifecycle’ ...
** package ‘lifecycle’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lifecycle)
* installing *source* package ‘askpass’ ...
** package ‘askpass’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c askpass.c -o askpass.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o askpass.so askpass.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-askpass/00new/askpass/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (askpass)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for curl-config... /usr/bin/curl-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
Version has a libidn field
Version has CURLOPT_URL
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Version has CURLINFO_TOTAL_TIME
Version has CURLINFO_NAMELOOKUP_TIME
Version has CURLINFO_CONNECT_TIME
Version has CURLINFO_PRETRANSFER_TIME
Version has CURLINFO_SIZE_UPLOAD
Version has CURLINFO_SIZE_DOWNLOAD
Version has CURLINFO_SPEED_DOWNLOAD
Version has CURLINFO_SPEED_UPLOAD
Version has CURLINFO_HEADER_SIZE
Version has CURLINFO_REQUEST_SIZE
Version has CURLINFO_SSL_VERIFYRESULT
Version has CURLINFO_FILETIME
Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD
Version has CURLINFO_CONTENT_LENGTH_UPLOAD
Version has CURLINFO_STARTTRANSFER_TIME
Version has CURLINFO_CONTENT_TYPE
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Version has CURLINFO_REDIRECT_COUNT
Version has CURLINFO_PRIVATE
Version has CURLINFO_HTTP_CONNECTCODE
Version has CURLINFO_HTTPAUTH_AVAIL
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Version has CURLINFO_OS_ERRNO
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Version has CURLINFO_COOKIELIST
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Version has CURLINFO_REDIRECT_URL
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Version has CURLINFO_APPCONNECT_TIME
Version has CURLINFO_CERTINFO
Version has CURLINFO_CONDITION_UNMET
Version has CURLOPT_WRITEDATA
Version has CURLOPT_KEYPASSWD
Version has CURLOPT_DIRLISTONLY
Version has CURLOPT_APPEND
Version has CURLOPT_KRBLEVEL
Version has CURLOPT_USE_SSL
Version has CURLOPT_TIMEOUT_MS
Version has CURLOPT_CONNECTTIMEOUT_MS
Version has CURLOPT_HTTP_TRANSFER_DECODING
Version has CURLOPT_HTTP_CONTENT_DECODING
Version has CURLOPT_NEW_FILE_PERMS
Version has CURLOPT_NEW_DIRECTORY_PERMS
Version has CURLOPT_POSTREDIR
Version has CURLOPT_OPENSOCKETFUNCTION
Version has CURLOPT_OPENSOCKETDATA
Version has CURLOPT_COPYPOSTFIELDS
Version has CURLOPT_PROXY_TRANSFER_MODE
Version has CURLOPT_SEEKFUNCTION
Version has CURLOPT_SEEKDATA
Version has CURLOPT_CRLFILE
Version has CURLOPT_ISSUERCERT
Version has CURLOPT_ADDRESS_SCOPE
Version has CURLOPT_CERTINFO
Version has CURLOPT_USERNAME
Version has CURLOPT_PASSWORD
Version has CURLOPT_PROXYUSERNAME
Version has CURLOPT_PROXYPASSWORD
Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5
Version has CURLOPT_NOPROXY
Version has CURLOPT_TFTP_BLKSIZE
Version has CURLOPT_SOCKS5_GSSAPI_SERVICE
Version has CURLOPT_SOCKS5_GSSAPI_NEC
Version has CURLOPT_PROTOCOLS
Version has CURLOPT_REDIR_PROTOCOLS
Version has CURLOPT_SSH_AUTH_TYPES
Version has CURLOPT_SSH_PUBLIC_KEYFILE
Version has CURLOPT_SSH_PRIVATE_KEYFILE
Version has CURLOPT_FTP_SSL_CCC
Version has CURLOPT_COOKIELIST
Version has CURLOPT_IGNORE_CONTENT_LENGTH
Version has CURLOPT_FTP_SKIP_PASV_IP
Version has CURLOPT_FTP_FILEMETHOD
Version has CURLOPT_LOCALPORT
Version has CURLOPT_LOCALPORTRANGE
Version has CURLOPT_CONNECT_ONLY
Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION
Version has CURLOPT_CONV_TO_NETWORK_FUNCTION
Version has CURLOPT_CONV_FROM_UTF8_FUNCTION
Version has CURLOPT_MAX_SEND_SPEED_LARGE
Version has CURLOPT_MAX_RECV_SPEED_LARGE
Version has CURLOPT_FTP_ALTERNATIVE_TO_USER
Version has CURLOPT_SOCKOPTFUNCTION
Version has CURLOPT_SOCKOPTDATA
Version has CURLOPT_SSL_SESSIONID_CACHE
libcurl version: libcurl 7.81.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curl.c -o curl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curlInit.c -o curlInit.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c curl_base64.c -o curl_base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c enums.c -o enums.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c json.c -o json.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c memoryManagement.c -o memoryManagement.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include    -fpic  -g -O2  -Wall -c myUTF8.c -o myUTF8.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-RCurl/00new/RCurl/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCurl)
* installing *source* package ‘cachem’ ...
** package ‘cachem’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o cachem.so cache.o init.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-cachem/00new/cachem/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cachem)
* installing *source* package ‘bit64’ ...
** package ‘bit64’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c bsearch.c -o bsearch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c cache.c -o cache.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c hash64.c -o hash64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integer64.c -o integer64.o
integer64.c: In function ‘runif_integer64’:
integer64.c:998:15: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  998 |     while( (*((long long *) &ii)) == NA_INTEGER64){
      |              ~^~~~~~~~~~~~~~~~~~
integer64.c:1006:36: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
 1006 |     ret[i] = min + ( (long long)(*((unsigned long long *)(&ii))) % d);
      |                                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort64.c -o sort64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sortuse64.c -o sortuse64.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o bit64.so bsearch.o cache.o hash64.o init.o integer64.o sort64.o sortuse64.o -lm -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-bit64/00new/bit64/libs
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bit64)
* installing *source* package ‘IRanges’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c CompressedList_class.c -o CompressedList_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Grouping_class.c -o Grouping_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IPosRanges_comparison.c -o IPosRanges_comparison.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_class.c -o IRanges_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c NCList.c -o NCList.o
NCList.c:1173:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function]
 1173 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
NCList.c:202:22: warning: ‘next_top_down’ defined but not used [-Wunused-function]
  202 | static const NCList *next_top_down(const NCList *nclist)
      |                      ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Ranges_class.c -o Ranges_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RleViews_utils.c -o RleViews_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’:
coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  579 |         if (*out_ranges_are_tiles && x_end != cvg_len)
      |             ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
coverage_methods.c:495:28: note: ‘x_end’ was declared here
  495 |             i, j, x_start, x_end, shift_elt, tmp;
      |                            ^~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function ‘C_find_partition_overlaps’:
extractListFragments.c:66:33: warning: ‘split_partitions_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   66 |                                 IntAE_insert_at(split_partitions_buf,
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   67 |                                         IntAE_get_nelt(split_partitions_buf),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   68 |                                         q_prev_end);
      |                                         ~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c inter_range_methods.c -o inter_range_methods.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IRanges)
* installing *source* package ‘vctrs’ ...
** package ‘vctrs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c altrep-rle.c -o altrep-rle.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c altrep.c -o altrep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c arg-counter.c -o arg-counter.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c arg.c -o arg.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c assert.c -o assert.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c bind.c -o bind.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c c-unchop.c -o c-unchop.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c c.c -o c.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c callables.c -o callables.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast-bare.c -o cast-bare.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast-dispatch.c -o cast-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c cast.c -o cast.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c compare.c -o compare.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c complete.c -o complete.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c conditions.c -o conditions.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c dictionary.c -o dictionary.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c dim.c -o dim.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c empty.c -o empty.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c equal.c -o equal.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c expand.c -o expand.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fields.c -o fields.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c fill.c -o fill.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c globals.c -o globals.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c group.c -o group.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c growable.c -o growable.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c interval.c -o interval.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c match-joint.c -o match-joint.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c match.c -o match.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c missing.c -o missing.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c names.c -o names.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-collate.c -o order-collate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-groups.c -o order-groups.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-sortedness.c -o order-sortedness.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order-truelength.c -o order-truelength.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c order.c -o order.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c poly-op.c -o poly-op.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c proxy-restore.c -o proxy-restore.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c proxy.c -o proxy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype-common.c -o ptype-common.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype.c -o ptype.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype2-dispatch.c -o ptype2-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c ptype2.c -o ptype2.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rank.c -o rank.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rep.c -o rep.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang-dev.c -o rlang-dev.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c rlang.c -o rlang.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c runs.c -o runs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c set.c -o set.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c shape.c -o shape.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c size-common.c -o size-common.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c size.c -o size.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-array.c -o slice-array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-assign-array.c -o slice-assign-array.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-assign.c -o slice-assign.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-chop.c -o slice-chop.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice-interleave.c -o slice-interleave.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c slice.c -o slice.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c split.c -o split.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c subscript-loc.c -o subscript-loc.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c subscript.c -o subscript.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c translate.c -o translate.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-data-frame.c -o type-data-frame.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-date-time.c -o type-date-time.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-factor.c -o type-factor.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-info.c -o type-info.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-integer64.c -o type-integer64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c type-tibble.c -o type-tibble.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typeof2-s3.c -o typeof2-s3.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c typeof2.c -o typeof2.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c unspecified.c -o unspecified.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils-dispatch.c -o utils-dispatch.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c vctrs-core.c -o vctrs-core.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I./rlang  -I/usr/local/include   -fvisibility=hidden -fpic  -g -O2  -Wall -c version.c -o version.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o vctrs.so altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-vctrs/00new/vctrs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vctrs)
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c aes.c -o aes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c base64.c -o base64.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bignum.c -o bignum.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c cert.c -o cert.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c compatibility.c -o compatibility.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c diffie.c -o diffie.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c envelope.c -o envelope.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c error.c -o error.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c hash.c -o hash.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c info.c -o info.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c keygen.c -o keygen.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c keys.c -o keys.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c onload.c -o onload.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c openssh.c -o openssh.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c password.c -o password.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pbkdf.c -o pbkdf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pem.c -o pem.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pkcs12.c -o pkcs12.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c pkcs7.c -o pkcs7.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c rand.c -o rand.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c rsa.c -o rsa.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c signing.c -o signing.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c ssl.c -o ssl.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c stream.c -o stream.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c write.c -o write.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c x25519.c -o x25519.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED  -I/usr/local/include    -fpic  -g -O2  -Wall -c bcrypt/blowfish.c -o bcrypt/blowfish.o
ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-openssl/00new/openssl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (openssl)
* installing *source* package ‘XVector’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function ‘RDS_extract_subarray’:
RDS_random_access.c:796:25: warning: unused variable ‘ans’ [-Wunused-variable]
  796 |         SEXP subscript, ans;
      |                         ^~~
RDS_random_access.c:793:18: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable]
  793 |         SEXPTYPE x_type;
      |                  ^~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_XVector.c -o R_init_XVector.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedDouble_class.c -o SharedDouble_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedInteger_class.c -o SharedInteger_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’:
SharedRaw_class.c:396:20: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable]
  396 |         SEXP dest, src_tag;
      |                    ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SharedVector_class.c -o SharedVector_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XDouble_class.c -o XDouble_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XInteger_class.c -o XInteger_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XRawList_comparison.c -o XRawList_comparison.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XRaw_class.c -o XRaw_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’:
XVectorList_class.c:459:17: warning: ‘lkup_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  459 |                 _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  460 |                         (char *) dest.ptr, dest.length,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  461 |                         src->elts, CharAE_get_nelt(src),
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  462 |                         lkup0, lkup_length);
      |                         ~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XVector_class.c -o XVector_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c io_utils.c -o io_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c slice_methods.c -o slice_methods.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vector_copy.c -o vector_copy.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function ‘get_which_min_from_Ints_holder’:
view_summarization_methods.c:219:45: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  219 |                 if (which_min == NA_INTEGER || x < cur_min) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c: In function ‘get_which_min_from_Doubles_holder’:
view_summarization_methods.c:246:45: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  246 |                 if (which_min == NA_INTEGER || x < cur_min) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c: In function ‘get_which_max_from_Ints_holder’:
view_summarization_methods.c:269:45: warning: ‘cur_max’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  269 |                 if (which_max == NA_INTEGER || x > cur_max) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c: In function ‘get_which_max_from_Doubles_holder’:
view_summarization_methods.c:296:45: warning: ‘cur_max’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  296 |                 if (which_max == NA_INTEGER || x > cur_max) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-XVector/00new/XVector/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XVector)
* installing *source* package ‘GenomeInfoDb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDb)
* installing *source* package ‘memoise’ ...
** package ‘memoise’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (memoise)
* installing *source* package ‘blob’ ...
** package ‘blob’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (blob)
* installing *source* package ‘httr’ ...
** package ‘httr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (httr)
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function]
  299 | static void BitMatrix_print(BitMatrix *bitmat)
      |             ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:184:27: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
  184 |         IntAE *poffsets, *poffsets_order;
      |                           ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’:
XStringSet_class.c:124:17: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  124 |                 _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |                                 INTEGER(start)[i], lkup0, lkup_len);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XString_class.c -o XString_class.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:155:29: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  155 |         INTEGER(ans_elt)[0] = score;
      |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:250:42: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  250 |                                 jPattern += indelWidthSubject;
      |                                 ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:231:63: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  231 |                         if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
      |                                                            ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:239:72: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  239 |                                                 mappedStringPtr[index] = gapCodeValue;
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
align_utils.c:232:78: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  232 |                                 if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
      |                                                                    ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’:
letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable]
  957 |   int x_width, y_width, x_length, *ans_mat, i, x_pos;
      |                                                ^~~~~
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
  956 |   SEXP ans, ans_dimnames;
      |             ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function]
    7 | static void test_match_pattern_indels(const char *p, const char *s,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  419 |                         ans_col += tb_length;
      |                         ~~~~~~~~^~~~~~~~~~~~
match_pdict.c:392:65: note: ‘ans_col’ was declared here
  392 |         int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
      |                                                                 ^~~~~~~
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  470 |                                 ans_elt += P_length;
      |                                 ~~~~~~~~^~~~~~~~~~~
match_pdict.c:441:64: note: ‘ans_elt’ was declared here
  441 |         int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
      |                                                                ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1031:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
 1031 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
match_pdict_ACtree2.c: In function ‘merge_pointers’:
match_pdict_ACtree2.c:1076:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
 1076 |         ACnode *node0, *node1, *node2;
      |                 ^~~~~
At top level:
match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
  602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function]
  139 | static void debug_node_counting_functions(int maxdepth)
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
match_pdict_Twobit.c: In function ‘build_Twobit’:
match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   75 |         PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos));
      |                           ^~~~~~~~~~~~~~~~~~~~~
match_pdict_Twobit.c:110:19: note: ‘twobit_sign2pos’ was declared here
  110 |         SEXP ans, twobit_sign2pos;
      |                   ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:653:56: warning: unused variable ‘ncol’ [-Wunused-variable]
  653 |         int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
      |                                                        ^~~~
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:713:13: warning: unused variable ‘nelt’ [-Wunused-variable]
  713 |         int nelt, nkey0, nkey1, nkey2, i, key;
      |             ^~~~
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:820:51: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:820:34: warning: unused variable ‘total_NFC’ [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:819:40: warning: unused variable ‘NFC’ [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                        ^~~
match_pdict_utils.c:819:33: warning: unused variable ‘nloci’ [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                                 ^~~~~
match_pdict_utils.c:819:27: warning: unused variable ‘ndup’ [-Wunused-variable]
  819 |         unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
      |                           ^~~~
At top level:
match_pdict_utils.c:820:34: warning: ‘total_NFC’ defined but not used [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                  ^~~~~~~~~
match_pdict_utils.c:820:51: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable]
  820 |         static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
      |                                                   ^~~~~~~~~~~~
match_pdict_utils.c:261:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
  261 | static void match_headtail_by_loc(const HeadTail *headtail,
      |             ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c read_fasta_files.c -o read_fasta_files.o
In function ‘new_FASTAloaderExt’,
    inlined from ‘read_fasta_files’ at read_fasta_files.c:430:15:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.ptr’ may be used uninitialized [-Wmaybe-uninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:182:24: note: ‘loader_ext’ declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
    inlined from ‘read_fasta_files’ at read_fasta_files.c:430:15:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.length’ may be used uninitialized [-Wmaybe-uninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:182:24: note: ‘loader_ext’ declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
    inlined from ‘read_fasta_blocks’ at read_fasta_files.c:596:15:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.ptr’ is used uninitialized [-Wuninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:182:24: note: ‘loader_ext’ declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
In function ‘new_FASTAloaderExt’,
    inlined from ‘read_fasta_blocks’ at read_fasta_files.c:596:15:
read_fasta_files.c:186:16: warning: ‘loader_ext.seq_elt_holder.length’ is used uninitialized [-Wuninitialized]
  186 |         return loader_ext;
      |                ^~~~~~~~~~
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:182:24: note: ‘loader_ext’ declared here
  182 |         FASTAloaderExt loader_ext;
      |                        ^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function ‘parse_FASTQ_file’:
read_fastq_files.c:392:28: warning: ‘dont_load’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  392 |                         if (dont_load || loader->new_empty_seq_hook == NULL)
      |                            ^
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:110:36: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  110 |                                 if (if_ambig == TRANSLATE_ERROR) {
      |                                    ^
translate.c:136:36: note: ‘if_ambig0’ was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                                    ^~~~~~~~~
translate.c:106:36: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  106 |                                 if (if_non_ambig == TRANSLATE_TO_X)
      |                                    ^
translate.c:136:21: note: ‘if_non_ambig0’ was declared here
  136 |         int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
      |                     ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:157:16: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  157 |         return twobit_sign;
      |                ^~~~~~~~~~~
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:164:19: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  164 |         int i, j, twobit_sign;
      |                   ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include' -I'/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/XVector/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
In file included from /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include/S4Vectors_defines.h:18,
                 from /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XString_xscat’:
/home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized]
   91 | #define NEW_RAW(n)              Rf_allocVector(RAWSXP,n)
      |                                 ^~~~~~~~~~~~~~
xscat.c:18:20: note: ‘ans_length’ was declared here
   18 |         int nargs, ans_length, tag_offset, j;
      |                    ^~~~~~~~~~
xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   52 |         PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag));
      |                       ^~~~~~~~~~~~~~~~~
In file included from /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/S4Vectors/include/S4Vectors_defines.h:18,
                 from /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XStringSet_xscat’:
/home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized]
   85 | #define NEW_INTEGER(n)          Rf_allocVector(INTSXP,n)
      |                                 ^~~~~~~~~~~~~~
xscat.c:66:39: note: ‘ans_length’ was declared here
   66 |         int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
      |                                       ^~~~~~~~~~
xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  108 |         PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width));
      |                       ^~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘pattern’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Biostrings)
ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘RSQLite’ had non-zero exit status
* installing *source* package ‘KEGGREST’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (KEGGREST)
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu95av2cdf’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpNAH8EI/downloaded_packages’
Warning: missing cdf environment! in show(AffyBatch)
AffyBatch object
size of arrays=640x640 features (38422 kb)
cdf=HG_U95Av2 (??? affyids)
number of samples=4
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’

trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.61.2.tar.gz'
Content type 'application/x-gzip' length 4359482 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331391 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘RSQLite’ had non-zero exit status
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu95av2cdf’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpNAH8EI/downloaded_packages’
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Calls: print ... <Anonymous> -> cat -> featureNames -> featureNames -> getCdfInfo
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘affy.Rnw’... failed
  ‘builtinMethods.Rnw’... OK
  ‘customMethods.Rnw’... OK
  ‘vim.Rnw’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘affy.Rnw’
  ...

The downloaded source packages are in
	‘/tmp/Rtmp5wBy6o/downloaded_packages’

  When sourcing ‘affy.R’:
Error: Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘affy.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’

trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.61.2.tar.gz'
Content type 'application/x-gzip' length 4359482 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331391 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘RSQLite’ had non-zero exit status
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/RtmpwV2zkR/RLIBS_7d719197e1ff0/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu95av2cdf’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmppHRQy2/downloaded_packages’

Error: processing vignette 'affy.Rnw' failed with diagnostics:
 chunk 6 
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed

--- failed re-building ‘affy.Rnw’

--- re-building ‘builtinMethods.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

--- finished re-building ‘builtinMethods.Rnw’

--- re-building ‘customMethods.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

--- finished re-building ‘customMethods.Rnw’

--- re-building ‘vim.Rnw’ using Sweave
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

--- finished re-building ‘vim.Rnw’

SUMMARY: processing the following file failed:
  ‘affy.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/affy.Rcheck/00check.log’
for details.
CHECK results for affy on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings
