methylKit 1.6.3
Altuna Akalin , Alexander Gosdschan
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/methylKit |
| Branch: RELEASE_3_7 |
| Last Commit: fd2779b |
| Last Changed Date: 2018-10-11 16:55:12 -0400 (Thu, 11 Oct 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/methylKit_1.6.3.tar.gz && rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylKit.buildbin-libdir methylKit_1.6.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL methylKit_1.6.3.zip && rm methylKit_1.6.3.tar.gz methylKit_1.6.3.zip
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install for i386
* installing *source* package 'methylKit' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:708:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:707:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:706:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:1027:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1026:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1025:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1254:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1253:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1252:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'methylKit'
finding HTML links ... done
PCASamples-methods html
adjustMethylC html
assocComp-methods html
bedgraph-methods html
calculateDiffMeth-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:179: file link 'pool' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:179: file link 'reorganize' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/calculateDiffMeth-methods.Rd:180: file link 'dataSim' in package 'methylKit' does not exist and so has been treated as a topic
calculateDiffMethDSS-methods html
clusterSamples-methods html
dataSim-methods html
diffMethPerChr-methods html
extract-methods html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/extract-methods.Rd:38: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
filterByCoverage-methods html
genomation-deprecated html
getAssembly-methods html
getContext-methods html
getCorrelation-methods html
getCoverageStats-methods html
getDBPath-methods html
getData-methods html
getMethylDiff-methods html
getMethylationStats-methods html
getSampleID-methods html
getTreatment-methods html
joinSegmentNeighbours html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/joinSegmentNeighbours.Rd:10: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/joinSegmentNeighbours.Rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
makeMethylDB-methods html
methRead-methods html
methSeg html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:11: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:14: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg.Rd:39: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methSeg2bed html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methSeg2bed.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylBase-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:63: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:63: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:64: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBase-class.Rd:70: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylBase.obj html
methylBaseDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:69: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:69: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:70: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylBaseDB-class.Rd:76: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylDiff-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:11: file link 'calculateDiffMeth' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:49: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:55: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:55: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiff-class.Rd:56: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
methylDiff.obj html
methylDiffDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:11: file link 'calculateDiffMeth' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:52: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:59: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:59: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylDiffDB-class.Rd:60: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
methylRaw-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:41: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:41: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:42: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRaw-class.Rd:48: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylRawDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:47: file link 'getData' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:47: file link 'getAssembly' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:48: file link 'getContext' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawDB-class.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
methylRawList-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawList-class.Rd:9: file link 'methylRaw' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawList-class.Rd:12: file link 'read' in package 'methylKit' does not exist and so has been treated as a topic
methylRawList.obj html
methylRawListDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawListDB-class.Rd:9: file link 'methylRawDB' in package 'methylKit' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp2HC1M8/R.INSTALL179c45446d24/methylKit/man/methylRawListDB-class.Rd:12: file link 'read' in package 'methylKit' does not exist and so has been treated as a topic
normalizeCoverage-methods html
percMethylation-methods html
pool-methods html
processBismarkAln-methods html
reconstruct-methods html
regionCounts html
finding level-2 HTML links ... done
removeComp-methods html
reorganize-methods html
select-methods html
selectByOverlap-methods html
show-methods html
tileMethylCounts-methods html
unite-methods html
updateMethObject html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'methylKit' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:708:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:707:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:706:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:1027:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1026:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1025:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1254:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1253:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1252:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov); std::fclose(out); }
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.6.3.zip
* DONE (methylKit)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'methylKit' successfully unpacked and MD5 sums checked
In R CMD INSTALL