methylKit 1.4.1
Altuna Akalin , Alexander Gosdschan
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/methylKit |
| Branch: RELEASE_3_6 |
| Last Commit: dd0dd4c |
| Last Changed Date: 2018-01-22 10:25:01 -0400 (Mon, 22 Jan 2018) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/methylKit_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=methylKit.buildbin-libdir --merge-multiarch methylKit_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL methylKit_1.4.1.zip && rm methylKit_1.4.1.tar.gz methylKit_1.4.1.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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/local323/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-3.6-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/i386
** R
** data
** inst
** preparing 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-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/calculateDiffMeth-methods.Rd:179: missing file link 'pool'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/calculateDiffMeth-methods.Rd:179: missing file link 'reorganize'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/calculateDiffMeth-methods.Rd:180: missing file link 'dataSim'
calculateDiffMethDSS-methods html
clusterSamples-methods html
dataSim-methods html
diffMethPerChr-methods html
extract-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/extract-methods.Rd:38: missing file link 'getData'
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-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/joinSegmentNeighbours.Rd:10: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/joinSegmentNeighbours.Rd:14: missing file link 'GRanges'
makeMethylDB-methods html
methRead-methods html
methSeg html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methSeg.Rd:11: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methSeg.Rd:14: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methSeg.Rd:39: missing file link 'GRanges'
methSeg2bed html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methSeg2bed.Rd:13: missing file link 'GRanges'
methylBase-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylBase-class.Rd:63: missing file link 'getData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylBase-class.Rd:63: missing file link 'getAssembly'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylBase-class.Rd:64: missing file link 'getContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylBase-class.Rd:70: missing file link 'GRanges'
methylBase.obj html
methylBaseDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylBaseDB-class.Rd:69: missing file link 'getData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylBaseDB-class.Rd:69: missing file link 'getAssembly'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylBaseDB-class.Rd:70: missing file link 'getContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylBaseDB-class.Rd:76: missing file link 'GRanges'
methylDiff-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiff-class.Rd:11: missing file link 'calculateDiffMeth'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiff-class.Rd:49: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiff-class.Rd:55: missing file link 'getData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiff-class.Rd:55: missing file link 'getAssembly'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiff-class.Rd:56: missing file link 'getContext'
methylDiff.obj html
methylDiffDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiffDB-class.Rd:11: missing file link 'calculateDiffMeth'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiffDB-class.Rd:52: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiffDB-class.Rd:59: missing file link 'getData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiffDB-class.Rd:59: missing file link 'getAssembly'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylDiffDB-class.Rd:60: missing file link 'getContext'
methylRaw-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRaw-class.Rd:41: missing file link 'getData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRaw-class.Rd:41: missing file link 'getAssembly'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRaw-class.Rd:42: missing file link 'getContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRaw-class.Rd:48: missing file link 'GRanges'
methylRawDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRawDB-class.Rd:47: missing file link 'getData'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRawDB-class.Rd:47: missing file link 'getAssembly'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRawDB-class.Rd:48: missing file link 'getContext'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRawDB-class.Rd:54: missing file link 'GRanges'
methylRawList-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRawList-class.Rd:9: missing file link 'methylRaw'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRawList-class.Rd:12: missing file link 'read'
methylRawList.obj html
methylRawListDB-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRawListDB-class.Rd:9: missing file link 'methylRawDB'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpWyXiqQ/R.INSTALLe0410d2f92/methylKit/man/methylRawListDB-class.Rd:12: missing file link 'read'
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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/local323/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˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/local323/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-3.6-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.4.1.zip
* DONE (methylKit)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'methylKit' successfully unpacked and MD5 sums checked
In R CMD INSTALL