QuasR 1.9.13
Michael Stadler
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QuasR | | Last Changed Rev: 107693 / Revision: 107696 | | Last Changed Date: 2015-08-23 03:47:36 -0700 (Sun, 23 Aug 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings QuasR_1.9.13.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/QuasR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.9.13’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘QuasR’ can be installed ... [27s/27s] 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘ShortRead:::.ShortReadQQA’ ‘ShortRead:::.qa_adapterContamination’
‘ShortRead:::.set_omp_threads’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call(ShortRead:::.set_omp_threads, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
createAuxAlignments: no visible global function definition for
‘makeCluster’
createAuxAlignments: no visible global function definition for
‘stopCluster’
createGenomicAlignments: no visible global function definition for
‘makeCluster’
createGenomicAlignments: no visible global function definition for
‘stopCluster’
createSeedList: no visible global function definition for
‘bsgenomeName’
getListOfBiocParallelParam: no visible global function definition for
‘registered’
qCount: no visible global function definition for ‘seqlevelsInUse’
qCount: no visible global function definition for ‘seqlevels’
qCount: no visible global function definition for ‘splitIndices’
qMeth: no visible global function definition for ‘seqlevels’
qProfile: no visible global function definition for ‘seqlevels’
samToSortedBamParallel: no visible global function definition for
‘makeCluster’
samToSortedBamParallel: no visible global function definition for
‘stopCluster’
test: no visible global function definition for ‘defineTestSuite’
test: no visible global function definition for ‘runTestSuite’
test: no visible global function definition for ‘printTextProtocol’
* 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 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘QuasR.pdf’ from 567Kb to 466Kb
consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/67s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
qCount 7.858 0.226 20.252
qMeth 0.893 0.141 13.012
qProject-class 0.461 0.064 9.969
qExportWig 0.137 0.019 9.965
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘QuasR_unit_tests.R’ [99s/311s]
[99s/311s] 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/QuasR.Rcheck/00check.log’
for details.
* installing *source* package ‘QuasR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c cat_bam.c -o cat_bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c count_alignments.c -o count_alignments.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c count_junctions.cpp -o count_junctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c export_wig.c -o export_wig.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c idxstats_bam.c -o idxstats_bam.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c profile_alignments.c -o profile_alignments.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c quantify_methylation.cpp -o quantify_methylation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-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-3.2-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c utilities.c -o utilities.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -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 /home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.2-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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)