QuasR 1.6.2
Michael Stadler
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/QuasR | | Last Changed Rev: 96362 / Revision: 102249 | | Last Changed Date: 2014-11-03 01:29:24 -0800 (Mon, 03 Nov 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
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### Running command:
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### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings QuasR_1.6.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/QuasR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.2’
* 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 ... [34s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicRanges’ ‘Rsamtools’
A package should be listed in only one of these fields.
* 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' calls in package code:
‘RUnit’ ‘rtracklayer’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘Rbowtie’ ‘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
align_RbowtieSpliced: no visible global function definition for
‘SpliceMap’
calcMmInformation: no visible global function definition for
‘seqlengths’
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’
detectVariantsBamfilesRegionsSingleChromosome: no visible global
function definition for ‘seqlengths’
grangesFromGff: no visible global function definition for ‘import.gff’
qCount: no visible global function definition for ‘seqlevelsInUse’
qCount: no visible global function definition for ‘seqlevels’
qCount: no visible global function definition for ‘seqlengths’
qCount: no visible global function definition for ‘splitIndices’
qMeth: no visible global function definition for ‘seqlevels’
qProfile: no visible global function definition for ‘seqlevels’
quantifyMethylationBamfilesRegionsSingleChromosome: no visible global
function definition for ‘seqlengths’
quantifyMethylationBamfilesRegionsSingleChromosomeAllele: no visible
global function definition for ‘seqlengths’
quantifyMethylationBamfilesRegionsSingleChromosomeSingleAlignments: no
visible global function definition for ‘seqlengths’
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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘QuasR/libs/QuasR.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘merge_reorder_sam.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/86s] WARNING
Found the following significant warnings:
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
qCount 2.433 0.256 22.871
qMeth 0.884 0.296 16.858
qProject-class 0.364 0.124 13.509
qExportWig 0.220 0.024 14.449
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘QuasR_unit_tests.R’ [96s/380s]
[96s/381s] 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
WARNING: There were 2 warnings.
NOTE: There were 5 notes.
See
‘/home/biocbuild/bbs-3.0-bioc/meat/QuasR.Rcheck/00check.log’
for details.
* installing *source* package ‘QuasR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c cat_bam.c -o cat_bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c count_alignments.c -o count_alignments.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c count_junctions.cpp -o count_junctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c export_wig.c -o export_wig.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c idxstats_bam.c -o idxstats_bam.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c profile_alignments.c -o profile_alignments.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c quantify_methylation.cpp -o quantify_methylation.o
quantify_methylation.cpp: In function ‘SEXPREC* quantify_methylation_singleAlignments(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
quantify_methylation.cpp:1070:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
quantify_methylation.cpp:1070:68: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/include" -fpic -g -O2 -Wall -c utilities.c -o utilities.o
g++ -shared -L/home/biocbuild/bbs-3.0-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 -lz /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.0-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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)