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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CSAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CSAR_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CSAR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CSAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CSAR' version '1.40.0'
* 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 whether package 'CSAR' can be installed ... OK
* 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 ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
mappedReads2Nhits: no visible global function definition for
  'chromosome'
mappedReads2Nhits: no visible global function definition for 'position'
Undefined global functions or variables:
  chromosome position
* checking Rd files ... OK
* 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/CSAR/libs/i386/CSAR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/CSAR/libs/x64/CSAR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
CSAR-package           20.09   0.07   20.16
getThreshold           18.80   0.10   18.89
permutatedWinScores    17.52   0.04   17.56
getPermutatedWinScores 17.11   0.04   17.15
genesWithPeaks          6.39   0.02    6.41
sigWin                  5.91   0.00    5.90
distance2Genes          5.33   0.01    5.34
ChIPseqScore            5.15   0.00    5.16
score2wig               5.04   0.01    5.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
permutatedWinScores    18.45   0.05   18.50
getThreshold           18.34   0.06   18.41
CSAR-package           16.72   0.03   16.75
getPermutatedWinScores 15.91   0.05   16.14
sigWin                  6.75   0.00    6.75
genesWithPeaks          6.67   0.00    6.69
distance2Genes          6.48   0.01    6.50
ChIPseqScore            5.19   0.00    5.19
score2wig               5.08   0.01    5.09
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/CSAR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CSAR_1.40.0.tar.gz && rm -rf CSAR.buildbin-libdir && mkdir CSAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CSAR.buildbin-libdir CSAR_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CSAR_1.40.0.zip && rm CSAR_1.40.0.tar.gz CSAR_1.40.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 25085  100 25085    0     0   381k      0 --:--:-- --:--:-- --:--:--  422k

install for i386

* installing *source* package 'CSAR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CSAR.c -o CSAR.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CSAR.buildbin-libdir/00LOCK-CSAR/00new/CSAR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CSAR'
    finding HTML links ... done
    CSAR-package                            html  
    ChIPseqScore                            html  
    distance2Genes                          html  
    genesWithPeaks                          html  
    getPermutatedWinScores                  html  
    getThreshold                            html  
    loadMappedReads                         html  
    mappedReads2Nhits                       html  
    permutatedWinScores                     html  
    sampleSEP3_test                         html  
    score2wig                               html  
    sigWin                                  html  
** 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

install for x64

* installing *source* package 'CSAR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CSAR.c -o CSAR.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CSAR.dll tmp.def CSAR.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CSAR.buildbin-libdir/CSAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CSAR' as CSAR_1.40.0.zip
* DONE (CSAR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CSAR' successfully unpacked and MD5 sums checked