Back to Multiple platform build/check report for BioC 3.7
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

INSTALL report for bamsignals on tokay2

This page was generated on 2018-10-17 08:40:10 -0400 (Wed, 17 Oct 2018).

Package 90/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bamsignals 1.12.1
Alessandro Mammana
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/bamsignals
Branch: RELEASE_3_7
Last Commit: 06b6282
Last Changed Date: 2018-05-31 19:52:28 -0400 (Thu, 31 May 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bamsignals
Version: 1.12.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/bamsignals_1.12.1.tar.gz && rm -rf bamsignals.buildbin-libdir && mkdir bamsignals.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bamsignals.buildbin-libdir bamsignals_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL bamsignals_1.12.1.zip && rm bamsignals_1.12.1.tar.gz bamsignals_1.12.1.zip
StartedAt: 2018-10-16 19:26:18 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:27:13 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 55.1 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/bamsignals_1.12.1.tar.gz && rm -rf bamsignals.buildbin-libdir && mkdir bamsignals.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bamsignals.buildbin-libdir bamsignals_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL bamsignals_1.12.1.zip && rm bamsignals_1.12.1.tar.gz bamsignals_1.12.1.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 2367k  100 2367k    0     0  27.9M      0 --:--:-- --:--:-- --:--:-- 30.0M

install for i386

* installing *source* package 'bamsignals' ...
** libs
C:/Rtools/mingw_32/bin/g++  -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 CountSignals.cpp -o CountSignals.o
C:/Rtools/mingw_32/bin/g++  -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++  -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 bamsignals.cpp -o bamsignals.o
bamsignals.cpp: In function 'bool writeSamAsBamAndIndex(const string&, const string&)':
bamsignals.cpp:516:31: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
     sam_hdr_write(out, header);
                               ^
bamsignals.cpp:521:36: warning: ignoring return value of 'int bam_write1(BGZF*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
         bam_write1(out->fp.bgzf, b); // write the alignment to `out'
                                    ^
bamsignals.cpp:530:40: warning: ignoring return value of 'int sam_index_build(const char*, int)', declared with attribute warn_unused_result [-Wunused-result]
     bam_index_build(bampath.c_str(), 0);
                                        ^
C:/Rtools/mingw_32/bin/gcc  -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"     -O3 -Wall  -std=gnu99 -mtune=generic -c bamsignals_init.c -o bamsignals_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o bamsignals.dll tmp.def CountSignals.o RcppExports.o bamsignals.o bamsignals_init.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/bamsignals.buildbin-libdir/bamsignals/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'bamsignals'
    finding HTML links ... done
    CountSignals-class                      html  
    as.list.CountSignals                    html  
    bamsignals-methods                      html  
    bamsignals                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'bamsignals' ...
** libs
C:/Rtools/mingw_64/bin/g++  -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 CountSignals.cpp -o CountSignals.o
C:/Rtools/mingw_64/bin/g++  -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++  -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 bamsignals.cpp -o bamsignals.o
bamsignals.cpp: In function 'bool writeSamAsBamAndIndex(const string&, const string&)':
bamsignals.cpp:516:31: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
     sam_hdr_write(out, header);
                               ^
bamsignals.cpp:521:36: warning: ignoring return value of 'int bam_write1(BGZF*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
         bam_write1(out->fp.bgzf, b); // write the alignment to `out'
                                    ^
bamsignals.cpp:530:40: warning: ignoring return value of 'int sam_index_build(const char*, int)', declared with attribute warn_unused_result [-Wunused-result]
     bam_index_build(bampath.c_str(), 0);
                                        ^
C:/Rtools/mingw_64/bin/gcc  -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  -std=gnu99 -mtune=generic -c bamsignals_init.c -o bamsignals_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o bamsignals.dll tmp.def CountSignals.o RcppExports.o bamsignals.o bamsignals_init.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/bamsignals.buildbin-libdir/bamsignals/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bamsignals' as bamsignals_1.12.1.zip
* DONE (bamsignals)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'bamsignals' successfully unpacked and MD5 sums checked
In R CMD INSTALL