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BioC 2.12: BUILD BIN report for casper on moscato2

This page was generated on 2013-10-09 09:39:15 -0700 (Wed, 09 Oct 2013).

Package 100/671HostnameOS / ArchBUILDCHECKBUILD BIN
casper 1.1.2
David Rossell
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/casper
Last Changed Rev: 78332 / Revision: 81334
Last Changed Date: 2013-07-11 06:04:00 -0700 (Thu, 11 Jul 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ]
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: casper
Version: 1.1.2
Command: rm -rf casper.buildbin-libdir && mkdir casper.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=casper.buildbin-libdir casper_1.1.2.tar.gz
StartedAt: 2013-10-09 04:56:52 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 04:59:45 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 172.5 seconds
RetCode: 0
Status:  OK  
PackageFile: casper_1.1.2.zip
PackageFileSize: 2.083 MiB

Command output


install for i386

* installing *source* package 'casper' ...
** libs
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c casper.cpp -o casper.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cstat.cpp -o cstat.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c dataframe.cpp -o dataframe.o
dataframe.cpp: In member function 'Variant* DataFrame::path2Variant(Fragment*)':
dataframe.cpp:271:2: warning: 'eid' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c discretedf.cpp -o discretedf.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c exon.cpp -o exon.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c fragFunc.c -o fragFunc.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c fragment.cpp -o fragment.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c functions.c -o functions.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c hash.c -o hash.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c join_exons.c -o join_exons.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c makeIslands.c -o makeIslands.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c model.cpp -o model.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c model_cmp.cpp -o model_cmp.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pathCounts.c -o pathCounts.o
pathCounts.c: In function 'pathCounts':
pathCounts.c:20:7: warning: variable 'totF' set but not used [-Wunused-but-set-variable]
pathCounts.c: In function 'sort2':
pathCounts.c:200:9: warning: variable 'res' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c procBam.c -o procBam.o
procBam.c: In function 'procBam':
procBam.c:15:43: warning: variable 'reads_size' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c rcasper.cpp -o rcasper.o
rcasper.cpp: In function 'SEXPREC* calcKnownSingle(double*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
rcasper.cpp:649:13: warning: variable 'f' set but not used [-Wunused-but-set-variable]
rcasper.cpp: In function 'SEXPREC* calcDenovoSingle(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
rcasper.cpp:965:57: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
rcasper.cpp:1025:30: warning: variable 'bestModelPrior' set but not used [-Wunused-but-set-variable]
rcasper.cpp:1189:15: warning: 'bestModel' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c seppel.cpp -o seppel.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c simReads.c -o simReads.o
simReads.c: In function 'casperSimC':
simReads.c:117:7: warning: variable 'l' set but not used [-Wunused-but-set-variable]
simReads.c:18:16: warning: variable 'ldd' set but not used [-Wunused-but-set-variable]
simReads.c:17:73: warning: variable 'ldlen' set but not used [-Wunused-but-set-variable]
simReads.c:144:36: warning: 'cigars' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c simReadsfunc.c -o simReadsfunc.o
simReadsfunc.c: In function 'build_path':
simReadsfunc.c:173:7: warning: variable 'chk' set but not used [-Wunused-but-set-variable]
simReadsfunc.c:163:43: warning: 'en' may be used uninitialized in this function [-Wuninitialized]
simReadsfunc.c:163:43: warning: 'rst' may be used uninitialized in this function [-Wuninitialized]
simReadsfunc.c:163:43: warning: 'ren' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c smartmodeldist.cpp -o smartmodeldist.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c uniqQname.c -o uniqQname.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c variant.cpp -o variant.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c variant_cmp.cpp -o variant_cmp.o
g++ -m32 -shared -s -static-libgcc -o casper.dll tmp.def casper.o cstat.o dataframe.o discretedf.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/casper.buildbin-libdir/casper/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'transcripts' in package 'casper'
Creating a generic function for 'plot' from package 'graphics' in package 'casper'
Creating a generic function for 'lines' from package 'graphics' in package 'casper'
Creating a generic function for 'coef' from package 'stats' in package 'casper'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'casper' ...
** libs
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c casper.cpp -o casper.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c cstat.cpp -o cstat.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c dataframe.cpp -o dataframe.o
dataframe.cpp: In member function 'Variant* DataFrame::path2Variant(Fragment*)':
dataframe.cpp:271:2: warning: 'eid' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c discretedf.cpp -o discretedf.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c exon.cpp -o exon.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c fragFunc.c -o fragFunc.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c fragment.cpp -o fragment.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c functions.c -o functions.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c hash.c -o hash.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c join_exons.c -o join_exons.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c makeIslands.c -o makeIslands.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c model.cpp -o model.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c model_cmp.cpp -o model_cmp.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pathCounts.c -o pathCounts.o
pathCounts.c: In function 'pathCounts':
pathCounts.c:20:7: warning: variable 'totF' set but not used [-Wunused-but-set-variable]
pathCounts.c: In function 'sort2':
pathCounts.c:200:9: warning: variable 'res' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c procBam.c -o procBam.o
procBam.c: In function 'procBam':
procBam.c:15:43: warning: variable 'reads_size' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c rcasper.cpp -o rcasper.o
rcasper.cpp: In function 'SEXPREC* calcKnownSingle(double*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
rcasper.cpp:649:13: warning: variable 'f' set but not used [-Wunused-but-set-variable]
rcasper.cpp: In function 'SEXPREC* calcDenovoSingle(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
rcasper.cpp:965:57: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
rcasper.cpp:1025:30: warning: variable 'bestModelPrior' set but not used [-Wunused-but-set-variable]
rcasper.cpp:1189:15: warning: 'bestModel' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c seppel.cpp -o seppel.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c simReads.c -o simReads.o
simReads.c: In function 'casperSimC':
simReads.c:117:7: warning: variable 'l' set but not used [-Wunused-but-set-variable]
simReads.c:18:16: warning: variable 'ldd' set but not used [-Wunused-but-set-variable]
simReads.c:17:73: warning: variable 'ldlen' set but not used [-Wunused-but-set-variable]
simReads.c:144:36: warning: 'cigars' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c simReadsfunc.c -o simReadsfunc.o
simReadsfunc.c: In function 'build_path':
simReadsfunc.c:173:7: warning: variable 'chk' set but not used [-Wunused-but-set-variable]
simReadsfunc.c:163:43: warning: 'en' may be used uninitialized in this function [-Wuninitialized]
simReadsfunc.c:163:43: warning: 'rst' may be used uninitialized in this function [-Wuninitialized]
simReadsfunc.c:163:43: warning: 'ren' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c smartmodeldist.cpp -o smartmodeldist.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c uniqQname.c -o uniqQname.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c variant.cpp -o variant.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/R/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c variant_cmp.cpp -o variant_cmp.o
g++ -m64 -shared -s -static-libgcc -o casper.dll tmp.def casper.o cstat.o dataframe.o discretedf.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.12-bioc/meat/casper.buildbin-libdir/casper/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'casper' as casper_1.1.2.zip
* DONE (casper)