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CHECK report for CNEr on malbec2

This page was generated on 2019-04-09 11:37:39 -0400 (Tue, 09 Apr 2019).

Package 297/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNEr 1.19.1
Ge Tan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/CNEr
Branch: master
Last Commit: 0753f3a
Last Changed Date: 2018-11-01 14:42:17 -0400 (Thu, 01 Nov 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: CNEr
Version: 1.19.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CNEr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CNEr_1.19.1.tar.gz
StartedAt: 2019-04-08 23:33:28 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:45:06 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 697.5 seconds
RetCode: 0
Status:  OK 
CheckDir: CNEr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CNEr.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CNEr_1.19.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CNEr.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CNEr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CNEr’ version ‘1.19.1’
* 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 ‘CNEr’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 18.3Mb
  sub-directories of 1Mb or more:
    extdata  15.9Mb
    libs      1.1Mb
* 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
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/CNEr/libs/CNEr.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

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 ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
makeGRBs     372.321  6.192 385.445
plotCNEWidth   7.657  0.016   7.672
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/CNEr.Rcheck/00check.log’
for details.



Installation output

CNEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CNEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CNEr’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c R_init_CNEr.c -o R_init_CNEr.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘bin_ranges_from_coord_range_standard’:
utils.c:50:7: warning: unused variable ‘_binNextShift’ [-Wunused-variable]
   int _binNextShift = binNextShift();
       ^˜˜˜˜˜˜˜˜˜˜˜˜
utils.c:49:7: warning: unused variable ‘_binFirstShift’ [-Wunused-variable]
   int _binFirstShift = binFirstShift();
       ^˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c io.c -o io.o
io.c: In function ‘myReadAxt’:
io.c:94:26: warning: unused variable ‘curAxt’ [-Wunused-variable]
   struct axt *axt=NULL, *curAxt;
                          ^˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ceScan.c -o ceScan.o
ceScan.c: In function ‘ceScan’:
ceScan.c:615:8: warning: unused variable ‘rest’ [-Wunused-variable]
   char rest, path[PATH_LEN];
        ^˜˜˜
ceScan.c:613:10: warning: unused variable ‘n’ [-Wunused-variable]
   int i, n;
          ^
ceScan.c: In function ‘freeSlThreshold’:
ceScan.c:674:17: warning: unused variable ‘CNE’ [-Wunused-variable]
   struct slCNE *CNE, *nextCNE, *el_CNE;
                 ^˜˜
ceScan.c:673:23: warning: unused variable ‘thresholds’ [-Wunused-variable]
   struct slThreshold *thresholds, *nextThreshold, *el_threshold;
                       ^˜˜˜˜˜˜˜˜˜
ceScan.c: In function ‘myCeScan’:
ceScan.c:868:28: warning: unused variable ‘i’ [-Wunused-variable]
   int nrCNE[nrThresholds], i;
                            ^
ceScan.c:868:7: warning: unused variable ‘nrCNE’ [-Wunused-variable]
   int nrCNE[nrThresholds], i;
       ^˜˜˜˜
ceScan.c:865:17: warning: unused variable ‘CNE’ [-Wunused-variable]
   struct slCNE *CNE;
                 ^˜˜
ceScan.c: In function ‘myCeScanFile’:
ceScan.c:898:7: warning: unused variable ‘nrThresholds’ [-Wunused-variable]
   int nrThresholds = GET_LENGTH(winSize);
       ^˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/axt.c -o ucsc/axt.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/chain.c -o ucsc/chain.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function ‘byteSwap64’:
ucsc/common.c:2846:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
 ˜˜˜˜˜˜˜^˜˜
ucsc/common.c:2847:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
 ˜˜˜˜˜˜˜^˜˜
ucsc/common.c:2848:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
 ˜˜˜˜˜˜˜^˜˜
ucsc/common.c:2849:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
 ˜˜˜˜˜˜˜^˜˜
ucsc/common.c: In function ‘byteSwapDouble’:
ucsc/common.c:2980:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[4] = u.bytes[3];
 ˜˜˜˜˜˜˜^˜˜
ucsc/common.c:2981:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[5] = u.bytes[2];
 ˜˜˜˜˜˜˜^˜˜
ucsc/common.c:2982:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[6] = u.bytes[1];
 ˜˜˜˜˜˜˜^˜˜
ucsc/common.c:2983:8: warning: array subscript is above array bounds [-Warray-bounds]
 v.bytes[7] = u.bytes[0];
 ˜˜˜˜˜˜˜^˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function ‘findHeadPolyTMaybeMask’:
ucsc/dnautil.c:942:5: warning: variable ‘pastPoly’ set but not used [-Wunused-but-set-variable]
 int pastPoly = 0;
     ^˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/errabort.c -o ucsc/errabort.o
ucsc/errabort.c:30:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=]
 static char const rcsid[] = "$Id: errabort.c,v 1.16 2010/01/12 18:16:27 markd Exp $";
                   ^˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/https.c -o ucsc/https.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/intExp.c -o ucsc/intExp.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/kxTok.c -o ucsc/kxTok.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/options.c -o ucsc/options.o
ucsc/options.c: In function ‘validateOption’:
ucsc/options.c:49:11: warning: variable ‘discardMe’ set but not used [-Wunused-but-set-variable]
 long long discardMe = 0;
           ^˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/sqlList.c -o ucsc/sqlList.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/os.c -o ucsc/os.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I/usr/local/include -g -fpic  -g -O2  -Wall -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o CNEr.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_CNEr.o utils.o io.o ceScan.o ucsc/axt.o ucsc/base64.o ucsc/binRange.o ucsc/bits.o ucsc/chain.o ucsc/_cheapcgi.o ucsc/cirTree.o ucsc/common.o ucsc/dlist.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/dystring.o ucsc/errabort.o ucsc/hash.o ucsc/https.o ucsc/intExp.o ucsc/kxTok.o ucsc/linefile.o ucsc/localmem.o ucsc/memalloc.o ucsc/obscure.o ucsc/options.o ucsc/pipeline.o ucsc/_portimpl.o ucsc/sqlList.o ucsc/sqlNum.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o -lz -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-CNEr/00new/CNEr/libs
** R
** data
** 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 (CNEr)

Tests output

CNEr.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(testthat)
> library(CNEr)

> 
> test_check("CNEr")
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 352
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 50
The number of axt files 1
The number of axt alignments is 352
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 86 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 25.629   0.608  26.229 

Example timings

CNEr.Rcheck/CNEr-Ex.timings

nameusersystemelapsed
AssemblyStats0.0150.0080.504
Axt-class0.8350.0200.855
Axt-util0.0310.0030.051
CNE-class0.1360.0040.140
CNEDanRer10Hg380.0060.0040.011
CNEDensity0.9950.0311.244
GRangePairs-class0.7900.0120.803
addAncestorGO000
axisTrack0.0050.0000.006
axtChain0.0000.0000.001
axtInfo0.0020.0000.002
binner0.0030.0000.003
blatCNE000
ceScan-methods1.5830.0471.691
chainMergeSort0.0000.0000.001
chainNetSyntenic0.0000.0000.001
chainPreNet0.0000.0000.001
cneFinalListDanRer10Hg380.0480.0040.052
cneMerge0.7430.0040.747
fetchChromSizes0.0010.0000.000
fixCoordinates0.4750.0040.478
grangesPairsForDotplot0.0020.0000.003
last0.0000.0000.001
lastz000
lavToPsl000
makeAncoraFiles0.0590.0040.063
makeAxtTracks0.3210.0240.345
makeCNEDensity000
makeGRBs372.321 6.192385.445
matchDistribution0.2460.0040.250
netToAxt0.0000.0000.001
orgKEGGIds2EntrezIDs000
plotCNEDistribution0.4630.0040.468
plotCNEWidth7.6570.0167.672
psubAxt0.2650.0040.269
read.rmMask.GRanges0.0160.0000.035
read.rmskFasta0.0240.0000.038
readAncora0.0660.0000.078
readAncoraIntoSQLite1.0870.0081.095
readAxt0.0400.0080.049
readBed0.0130.0000.013
readCNERangesFromSQLite0.1570.0040.160
reverseCigar0.0010.0000.002
saveCNEToSQLite0.1290.0000.129
scoringMatrix0.0000.0000.001
subAxt-methods0.8850.0040.890
syntenicDotplot1.7700.2792.200
writeAxt0.0530.0000.053