methylKit 1.3.0
Altuna Akalin
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylKit | | Last Changed Rev: 129129 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | 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_1.3.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=methylKit.buildbin-libdir --merge-multiarch methylKit_1.3.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL methylKit_1.3.0.zip && rm methylKit_1.3.0.tar.gz methylKit_1.3.0.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=core2 -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=core2 -c methCall.cpp -o methCall.o
methCall.cpp: In function 'void processCigar(std::string, std::string&, std::string&)':
methCall.cpp:492:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i < insPos.size();i++){
^
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:635:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i=0; i < quals.length(); i++)
^
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:813:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i < len_cigar; i++ ) {
^
methCall.cpp:909:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i=0; i < quals.length(); i++)
^
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1089:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i=0; i < quals.length(); i++)
^
methCall.cpp:1093:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( ( (gbases[i] == 'C') && (i==quals.length()) ) && ( gbases.substr(i-1,4) == "CCGG" ) ) { continue;}
^
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:639:7: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
if( strand == '+') { key = "F|"+ chr+"|"+std::to_string(static_cast<long long>(start+i)); }
^
methCall.cpp:653:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:652:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:651:81: 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:913:7: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
if( strand == '+') { key = "F|"+ chr+"|"+std::to_string(static_cast<long long>(start+i)); }
^
methCall.cpp:927:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:926:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:925:81: 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:1111:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1110:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1109:81: 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
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=core2 -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=core2 -c methCall.cpp -o methCall.o
methCall.cpp: In function 'void processCigar(std::string, std::string&, std::string&)':
methCall.cpp:492:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i < insPos.size();i++){
^
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:635:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i=0; i < quals.length(); i++)
^
methCall.cpp: In function 'int process_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:813:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (i = 1; i < len_cigar; i++ ) {
^
methCall.cpp:909:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i=0; i < quals.length(); i++)
^
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1089:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i=0; i < quals.length(); i++)
^
methCall.cpp:1093:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if( ( (gbases[i] == 'C') && (i==quals.length()) ) && ( gbases.substr(i-1,4) == "CCGG" ) ) { continue;}
^
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:639:7: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
if( strand == '+') { key = "F|"+ chr+"|"+std::to_string(static_cast<long long>(start+i)); }
^
methCall.cpp:653:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:652:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:651:81: 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:913:7: warning: 'strand' may be used uninitialized in this function [-Wmaybe-uninitialized]
if( strand == '+') { key = "F|"+ chr+"|"+std::to_string(static_cast<long long>(start+i)); }
^
methCall.cpp:927:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:926:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:925:81: 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:1111:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
^
methCall.cpp:1110:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
^
methCall.cpp:1109:81: 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_1.3.0.zip
* DONE (methylKit)
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'methylKit' successfully unpacked and MD5 sums checked