BioC 3.0: CHECK report for QuasR on moscato1
This page was generated on 2015-04-10 09:48:31 -0700 (Fri, 10 Apr 2015).
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 |
Summary
| Package: QuasR
|
| Version: 1.6.2
|
| Command: rm -rf QuasR.buildbin-libdir QuasR.Rcheck && mkdir QuasR.buildbin-libdir QuasR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QuasR.buildbin-libdir QuasR_1.6.2.tar.gz >QuasR.Rcheck\00install.out 2>&1 && cp QuasR.Rcheck\00install.out QuasR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=QuasR.buildbin-libdir --install="check:QuasR-install.out" --force-multiarch --no-vignettes --timings QuasR_1.6.2.tar.gz
|
| StartedAt: 2015-04-10 04:35:51 -0700 (Fri, 10 Apr 2015)
|
| EndedAt: 2015-04-10 05:07:07 -0700 (Fri, 10 Apr 2015)
|
| EllapsedTime: 1875.2 seconds
|
| RetCode: 0
|
| Status: WARNINGS
|
| CheckDir: QuasR.Rcheck
|
| Warnings: 3
|
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf QuasR.buildbin-libdir QuasR.Rcheck && mkdir QuasR.buildbin-libdir QuasR.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QuasR.buildbin-libdir QuasR_1.6.2.tar.gz >QuasR.Rcheck\00install.out 2>&1 && cp QuasR.Rcheck\00install.out QuasR-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=QuasR.buildbin-libdir --install="check:QuasR-install.out" --force-multiarch --no-vignettes --timings QuasR_1.6.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/QuasR.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'QuasR' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-3.0-bioc/meat/QuasR.buildbin-libdir/QuasR/libs/i386/QuasR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
File 'D:/biocbld/bbs-3.0-bioc/meat/QuasR.buildbin-libdir/QuasR/libs/x64/QuasR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
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.
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [130s] 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 2.73 0.31 38.96
qMeth 0.64 0.09 22.94
qProject-class 0.26 0.08 21.07
qExportWig 0.27 0.02 19.70
** running examples for arch 'x64' ... [134s] 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 2.50 0.30 45.01
qMeth 0.86 0.13 25.60
qProject-class 0.31 0.05 17.97
qExportWig 0.17 0.04 18.93
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'QuasR_unit_tests.R' [520s]
[520s] OK
** running tests for arch 'x64' ...
Running 'QuasR_unit_tests.R' [585s]
[586s] 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 3 warnings.
NOTE: There were 5 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/QuasR.Rcheck/00check.log'
for details.
QuasR.Rcheck/00install.out:
install for i386
* installing *source* package 'QuasR' ...
** libs
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c cat_bam.c -o cat_bam.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c count_alignments.c -o count_alignments.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c count_junctions.cpp -o count_junctions.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c export_wig.c -o export_wig.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c idxstats_bam.c -o idxstats_bam.o
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c profile_alignments.c -o profile_alignments.o
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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 -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c split_sam_chr.c -o split_sam_chr.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
g++ -m32 -shared -s -static-libgcc -o QuasR.dll tmp.def 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 D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/QuasR.buildbin-libdir/QuasR/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'QuasR' ...
** libs
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c cat_bam.c -o cat_bam.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c count_alignments.c -o count_alignments.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c count_junctions.cpp -o count_junctions.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c export_wig.c -o export_wig.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c idxstats_bam.c -o idxstats_bam.o
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c profile_alignments.c -o profile_alignments.o
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -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 -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c split_sam_chr.c -o split_sam_chr.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
g++ -m64 -shared -s -static-libgcc -o QuasR.dll tmp.def 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 D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/QuasR.buildbin-libdir/QuasR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QuasR' as QuasR_1.6.2.zip
* DONE (QuasR)
QuasR.Rcheck/examples_i386/QuasR-Ex.timings:
| name | user | system | elapsed
|
| QuasR-package | 0 | 0 | 0 |
|
| alignmentStats | 0 | 0 | 0 |
|
| preprocessReads | 2.22 | 0.05 | 2.56 |
|
| qAlign | 0 | 0 | 0 |
|
| qCount | 2.73 | 0.31 | 38.96 |
|
| qExportWig | 0.27 | 0.02 | 19.70 |
|
| qMeth | 0.64 | 0.09 | 22.94 |
|
| qProfile | 0.64 | 0.03 | 1.65 |
|
| qProject-class | 0.26 | 0.08 | 21.07 |
|
| qQCReport | 2.67 | 0.05 | 2.92 |
|
QuasR.Rcheck/examples_x64/QuasR-Ex.timings:
| name | user | system | elapsed
|
| QuasR-package | 0 | 0 | 0 |
|
| alignmentStats | 0 | 0 | 0 |
|
| preprocessReads | 1.98 | 0.08 | 2.98 |
|
| qAlign | 0 | 0 | 0 |
|
| qCount | 2.50 | 0.30 | 45.01 |
|
| qExportWig | 0.17 | 0.04 | 18.93 |
|
| qMeth | 0.86 | 0.13 | 25.60 |
|
| qProfile | 0.66 | 0.04 | 3.02 |
|
| qProject-class | 0.31 | 0.05 | 17.97 |
|
| qQCReport | 3.25 | 0.06 | 3.39 |
|