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BioC 3.5: INSTALL report for methylKit on tokay2

This page was generated on 2017-08-16 13:25:59 -0400 (Wed, 16 Aug 2017).

Package 805/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.2.0
Altuna Akalin
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/methylKit
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylKit
Version: 1.2.0
Command: rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/methylKit_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=methylKit.buildbin-libdir --merge-multiarch methylKit_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL methylKit_1.2.0.zip && rm methylKit_1.2.0.tar.gz methylKit_1.2.0.zip
StartedAt: 2017-08-15 18:32:48 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:34:45 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 116.4 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/methylKit_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=methylKit.buildbin-libdir --merge-multiarch methylKit_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL methylKit_1.2.0.zip  && rm methylKit_1.2.0.tar.gz methylKit_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  589k  100  589k    0     0  12.7M      0 --:--:-- --:--:-- --:--:-- 13.0M

install for i386

* installing *source* package 'methylKit' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.5-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˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.5-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-3.5-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.5-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˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.5-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-3.5-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.2.0.zip
* DONE (methylKit)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'methylKit' successfully unpacked and MD5 sums checked