QuasR 0.99.3
Michael Stadler
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QuasR | | Last Changed Rev: 72518 / Revision: 72575 | | Last Changed Date: 2013-01-14 15:50:17 -0800 (Mon, 14 Jan 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | ERROR | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ ERROR ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/QuasR.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QuasR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuasR’ version ‘0.99.3’
* 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 ‘QuasR’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qCount 4.392 0.356 30.470
qMeth 1.552 0.492 20.030
qProject-class 0.980 0.228 15.307
qExportWig 0.828 0.036 15.802
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘QuasR_unit_tests.R’
ERROR
Running the tests in ‘tests/QuasR_unit_tests.R’ failed.
Last 13 lines of output:
QuasR RUnit Tests - 59 test functions, 0 errors, 1 failure
FAILURE in test_bisulfit_single: Error in checkTrue(all(ifelse(readInfo[8] == "l", readInfo[, 3], readInfo[, :
Test not TRUE
Test left read position
Test files with failing tests
test_qAlign.R
test_bisulfit_single
Error in QuasR:::test() : unit tests failed for package QuasR
Execution halted
* installing *source* package ‘QuasR’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c R_init_QuasR.cpp -o R_init_QuasR.o
In file included from idxstats_bam.h:6:0,
from R_init_QuasR.cpp:14:
/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include/samtools/ksort.h:68:0: warning: "_SVID_SOURCE" redefined
/usr/include/features.h:168:0: note: this is the location of the previous definition
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c cat_bam.c -o cat_bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c count_alignments.c -o count_alignments.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c count_alignments_subregions.c -o count_alignments_subregions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c export_wig.c -o export_wig.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c idxstats_bam.c -o idxstats_bam.o
In file included from idxstats_bam.h:6:0,
from idxstats_bam.c:8:
/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include/samtools/ksort.h:68:0: warning: "_SVID_SOURCE" redefined
/usr/include/features.h:180:0: note: this is the location of the previous definition
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c profile_alignments.c -o profile_alignments.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c quantify_methylation.cpp -o quantify_methylation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c split_sam_chr.c -o split_sam_chr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -c utilities.c -o utilities.o
g++ -shared -L/usr/local/lib64 -o QuasR.so R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o -lz /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/QuasR.Rcheck/QuasR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘QuasR-Overview.Rnw’
** testing if installed package can be loaded
* DONE (QuasR)