QuasR 1.0.9
Michael Stadler
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/QuasR | | Last Changed Rev: 80833 / Revision: 81334 | | Last Changed Date: 2013-09-27 06:44:07 -0700 (Fri, 27 Sep 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/QuasR.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.0.9’
* 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 ... [52s/53s] 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 ... [40s/126s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessReads 7.116 0.076 7.141
qCount 4.216 0.532 29.755
qMeth 1.860 0.704 26.031
qProject-class 0.705 0.344 19.655
qExportWig 0.336 0.044 19.018
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘QuasR_unit_tests.R’ [4m/14m]
[4m/14m] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
* 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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c R_init_QuasR.cpp -o R_init_QuasR.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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c count_alignments_subregions.c -o count_alignments_subregions.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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c count_junctions.cpp -o count_junctions.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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c idxstats_bam.c -o idxstats_bam.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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c quantify_methylation.cpp -o quantify_methylation.o
quantify_methylation.cpp: In function ‘int addHitToCounts(const bam1_t*, void*)’:
quantify_methylation.cpp:85:101: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
quantify_methylation.cpp: In function ‘int addHitToSNP(const bam1_t*, void*)’:
quantify_methylation.cpp:136:103: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
quantify_methylation.cpp: In function ‘int addHitToCountsAllele(const bam1_t*, void*)’:
quantify_methylation.cpp:183:101: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c utilities.c -o utilities.o
g++ -shared -L/usr/local/lib -o QuasR.so R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.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 /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /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
** testing if installed package can be loaded
* DONE (QuasR)