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INSTALL report for bamsignals on tokay1

This page was generated on 2020-08-12 11:43:03 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE bamsignals PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 106/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bamsignals 1.21.1
Johannes Helmuth
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/bamsignals
Branch: master
Last Commit: 026c62d
Last Changed Date: 2020-07-14 16:03:36 -0400 (Tue, 14 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bamsignals
Version: 1.21.1
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/bamsignals_1.21.1.tar.gz && rm -rf bamsignals.buildbin-libdir && mkdir bamsignals.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bamsignals.buildbin-libdir bamsignals_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL bamsignals_1.21.1.zip && rm bamsignals_1.21.1.tar.gz bamsignals_1.21.1.zip
StartedAt: 2020-08-11 17:27:06 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 17:30:11 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 185.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/bamsignals_1.21.1.tar.gz && rm -rf bamsignals.buildbin-libdir && mkdir bamsignals.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=bamsignals.buildbin-libdir bamsignals_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL bamsignals_1.21.1.zip && rm bamsignals_1.21.1.tar.gz bamsignals_1.21.1.zip
###
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100 2366k  100 2366k    0     0  26.6M      0 --:--:-- --:--:-- --:--:-- 27.8M

install for i386

* installing *source* package 'bamsignals' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CountSignals.cpp -o CountSignals.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bamsignals.cpp -o bamsignals.o
bamsignals.cpp: In function 'bool writeSamAsBamAndIndex(const string&, const string&)':
bamsignals.cpp:499:9: warning: variable 'iorval' set but not used [-Wunused-but-set-variable]
     int iorval;
         ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bamsignals_init.c -o bamsignals_init.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o bamsignals.dll tmp.def CountSignals.o RcppExports.o bamsignals.o bamsignals_init.o C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/bamsignals.buildbin-libdir/00LOCK-bamsignals/00new/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 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 'bamsignals' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CountSignals.cpp -o CountSignals.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c bamsignals.cpp -o bamsignals.o
bamsignals.cpp: In function 'bool writeSamAsBamAndIndex(const string&, const string&)':
bamsignals.cpp:499:9: warning: variable 'iorval' set but not used [-Wunused-but-set-variable]
     int iorval;
         ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bamsignals_init.c -o bamsignals_init.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o bamsignals.dll tmp.def CountSignals.o RcppExports.o bamsignals.o bamsignals_init.o C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/bamsignals.buildbin-libdir/bamsignals/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bamsignals' as bamsignals_1.21.1.zip
* DONE (bamsignals)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'bamsignals' successfully unpacked and MD5 sums checked