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BioC 3.4: INSTALL report for GenomicRanges on moscato1

This page was generated on 2016-09-21 03:42:59 -0700 (Wed, 21 Sep 2016).

Package 497/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicRanges 1.25.94
Bioconductor Package Maintainer
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges
Last Changed Rev: 120818 / Revision: 121152
Last Changed Date: 2016-09-08 20:17:31 -0700 (Thu, 08 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicRanges
Version: 1.25.94
Command: rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/GenomicRanges_1.25.94.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicRanges.buildbin-libdir --merge-multiarch GenomicRanges_1.25.94.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.25.94.zip && rm GenomicRanges_1.25.94.tar.gz GenomicRanges_1.25.94.zip
StartedAt: 2016-09-19 20:48:08 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:48:43 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 34.8 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 http://zin1/BBS/3.4/bioc/src/contrib/GenomicRanges_1.25.94.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=GenomicRanges.buildbin-libdir --merge-multiarch GenomicRanges_1.25.94.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL GenomicRanges_1.25.94.zip  && rm GenomicRanges_1.25.94.tar.gz GenomicRanges_1.25.94.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  142k  100  142k    0     0  7929k      0 --:--:-- --:--:-- --:--:-- 10.7M

install for i386

* installing *source* package 'GenomicRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicRanges' as GenomicRanges_1.25.94.zip
* DONE (GenomicRanges)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'GenomicRanges' successfully unpacked and MD5 sums checked