Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.1: INSTALL report for GenomicAlignments on moscato2

This page was generated on 2015-10-09 09:30:49 -0700 (Fri, 09 Oct 2015).

Package 396/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicAlignments 1.4.2
Bioconductor Package Maintainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GenomicAlignments
Last Changed Rev: 109036 / Revision: 109384
Last Changed Date: 2015-09-30 17:42:34 -0700 (Wed, 30 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: GenomicAlignments
Version: 1.4.2
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/GenomicAlignments_1.4.2.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch GenomicAlignments_1.4.2.tar.gz && rm GenomicAlignments_1.4.2.tar.gz
StartedAt: 2015-10-08 18:49:00 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 18:50:13 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 72.9 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/GenomicAlignments_1.4.2.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch GenomicAlignments_1.4.2.tar.gz && rm GenomicAlignments_1.4.2.tar.gz
###
##############################################################################
##############################################################################




install for i386

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'GenomicAlignments' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:678:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:676:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:541:2: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:587:12: note: 'ans_breakpoints' was declared here
cigar_utils.c:672:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:736:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_narrow':
cigar_utils.c:889:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:857:7: note: 'OP' was declared here
cigar_utils.c:881:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:856:17: note: 'OPL' was declared here
cigar_utils.c: In function 'cigar_qnarrow':
cigar_utils.c:1073:24: warning: 'OP' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1041:7: note: 'OP' was declared here
cigar_utils.c:1065:8: warning: 'OPL' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:1040:17: note: 'OPL' was declared here
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_query':
coordinate_mapping_methods.c:64:26: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:180:17: warning: 'out_nelt0' may be used uninitialized in this function [-Wuninitialized]
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
gcc -m32 -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/GenomicAlignments/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'GenomicAlignments' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:678:9: warning: 'f_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:676:16: warning: 'breakpoint' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:541:2: warning: 'ans_breakpoints' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c:587:12: note: 'ans_breakpoints' was declared here
cigar_utils.c:672:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:736:12: warning: 'flag_elt' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_query':
coordinate_mapping_methods.c:64:26: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -m64 -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/GenomicAlignments/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (GenomicAlignments)