QuasR 1.13.2
Michael Stadler
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QuasR | | Last Changed Rev: 119108 / Revision: 121152 | | Last Changed Date: 2016-07-04 00:08:52 -0700 (Mon, 04 Jul 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### D:\biocbld\bbs-3.4-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --no-vignettes --timings QuasR_1.13.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-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 '1.13.2'
* 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 ... 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 whether package 'QuasR' can be installed ... WARNING
Found the following significant warnings:
Warning: failed to assign RegisteredNativeSymbol for idxstatsBam to idxstatsBam since idxstatsBam is already defined in the 'QuasR' namespace
See 'D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00install.out' for details.
* 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 ... NOTE
Warning: failed to assign RegisteredNativeSymbol for idxstatsBam to idxstatsBam since idxstatsBam is already defined in the 'QuasR' namespace
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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.
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
test: no visible global function definition for 'defineTestSuite'
test: no visible global function definition for 'runTestSuite'
test: no visible global function definition for 'printTextProtocol'
Undefined global functions or variables:
defineTestSuite printTextProtocol runTestSuite
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qCount 5.82 0.34 31.67
qMeth 0.64 0.04 19.93
qProject-class 0.27 0.06 14.26
qExportWig 0.26 0.00 16.94
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'QuasR_unit_tests.R'
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: 1 WARNING, 5 NOTEs
See
'D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00check.log'
for details.
* installing *source* package 'QuasR' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c R_init_QuasR.cpp -o R_init_QuasR.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c cat_bam.c -o cat_bam.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c count_alignments.c -o count_alignments.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c count_alignments_subregions.c -o count_alignments_subregions.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c count_junctions.cpp -o count_junctions.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c export_wig.c -o export_wig.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c idxstats_bam.c -o idxstats_bam.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c profile_alignments.c -o profile_alignments.o
C:/Rtools/mingw_64/bin/g++ -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c quantify_methylation.cpp -o quantify_methylation.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c split_sam_chr.c -o split_sam_chr.o
C:/Rtools/mingw_64/bin/gcc -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/include" -I"c:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/g++ -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-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/R_init_QuasR.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/cat_bam.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/convert_reads_id_bis_rc.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/count_alignments.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/count_alignments_subregions.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/count_junctions.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/export_wig.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/extract_unmapped_reads.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/idxstats_bam.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/merge_reorder_sam.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/nucleotide_alignment_frequencies.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/profile_alignments.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/quantify_methylation.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/remove_unmapped_from_sam.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/split_sam_chr.o: File format not recognized
C:\Rtools\mingw_32\bin\nm.exe: D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/00_pkg_src/QuasR/src/utilities.o: File format not recognized
There were 16 warnings (use warnings() to see them)
installing to D:/biocbld/bbs-3.4-bioc/meat/QuasR.Rcheck/QuasR/libs/x64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: failed to assign RegisteredNativeSymbol for idxstatsBam to idxstatsBam since idxstatsBam is already defined in the 'QuasR' namespace
* DONE (QuasR)