methylKit 1.14.2
Altuna Akalin , Alexander Gosdschan
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/methylKit |
| Branch: RELEASE_3_11 |
| Last Commit: a4a2fdf |
| Last Changed Date: 2020-05-20 12:13:42 -0400 (Wed, 20 May 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| machv2 | macOS 10.14.6 Mojave / 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/3.11/bioc/src/contrib/methylKit_1.14.2.tar.gz && rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylKit.buildbin-libdir methylKit_1.14.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL methylKit_1.14.2.zip && rm methylKit_1.14.2.tar.gz methylKit_1.14.2.zip
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install for i386
* installing *source* package 'methylKit' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int)':
methCall.cpp:678:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:677:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:676:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function 'int process_bam(std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int)':
methCall.cpp:997:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:996:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1025:76: 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::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)':
methCall.cpp:1220:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1219:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1218:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/methylKit.buildbin-libdir/00LOCK-methylKit/00new/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
calculateDiffMethDSS-methods html
clusterSamples-methods html
dataSim-methods html
diffMethPerChr-methods html
extract-methods html
filterByCoverage-methods 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
makeMethylDB-methods html
methRead-methods html
methSeg html
finding level-2 HTML links ... done
methSeg2bed html
methylBase-class html
methylBase.obj html
methylBaseDB-class html
methylDiff-class html
methylDiff.obj html
methylDiffDB-class html
methylKit-defunct html
methylRaw-class html
methylRawDB-class html
methylRawList-class html
methylRawList.obj html
methylRawListDB-class html
normalizeCoverage-methods html
percMethylation-methods html
pool-methods html
processBismarkAln-methods html
readMethylDB-methods html
reconstruct-methods html
regionCounts html
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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'methylKit' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int)':
methCall.cpp:678:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:677:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:676:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function 'int process_bam(std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int)':
methCall.cpp:997:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:996:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1025:76: 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::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)':
methCall.cpp:1220:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1219:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1218:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.14.2.zip
* DONE (methylKit)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'methylKit' successfully unpacked and MD5 sums checked