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BioC 3.6: INSTALL report for GenomicRanges on tokay1

This page was generated on 2017-08-16 13:28:52 -0400 (Wed, 16 Aug 2017).

Package 550/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.29.12
Bioconductor Package Maintainer
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges
Last Changed Rev: 131619 / Revision: 131943
Last Changed Date: 2017-07-27 14:07:28 -0400 (Thu, 27 Jul 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] TIMEOUT  skipped  skipped 
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicRanges
Version: 1.29.12
Command: rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/GenomicRanges_1.29.12.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicRanges.buildbin-libdir --merge-multiarch GenomicRanges_1.29.12.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.29.12.zip && rm GenomicRanges_1.29.12.tar.gz GenomicRanges_1.29.12.zip
StartedAt: 2017-08-15 18:20:47 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:21:51 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 63.7 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir  && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/GenomicRanges_1.29.12.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicRanges.buildbin-libdir --merge-multiarch GenomicRanges_1.29.12.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.29.12.zip  && rm GenomicRanges_1.29.12.tar.gz GenomicRanges_1.29.12.zip
###
##############################################################################
##############################################################################


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100  145k  100  145k    0     0   393k      0 --:--:-- --:--:-- --:--:--  397k

install for i386

* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -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/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
** R
** 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 'GenomicRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/IRanges/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:143:38: warning: 'end' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:24: note: 'end' was declared here
  int nexons, j, start, end, width;
                        ^
transcript_utils.c:143:38: warning: 'start' may be used uninitialized in this function [-Wmaybe-uninitialized]
  return on_minus_strand ? end - tloc : start + tloc;
                                      ^
transcript_utils.c:120:17: note: 'start' was declared here
  int nexons, j, start, end, width;
                 ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GenomicRanges.dll tmp.def IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -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/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.29.12.zip
* DONE (GenomicRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'GenomicRanges' successfully unpacked and MD5 sums checked