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Package 129/514HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.0.0
Erik Wright
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/DECIPHER
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DECIPHER
Version: 1.0.0
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.0.0.tar.gz >DECIPHER-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=DECIPHER.buildbin-libdir --install="check:DECIPHER-install.out" --force-multiarch --no-vignettes --timings DECIPHER_1.0.0.tar.gz && mv DECIPHER.buildbin-libdir/* DECIPHER.Rcheck/ && rmdir DECIPHER.buildbin-libdir
StartedAt: 2012-03-24 01:06:48 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:08:56 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 127.2 seconds
RetCode: 0
Status:  OK  
CheckDir: DECIPHER.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/DECIPHER.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DECIPHER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DECIPHER' version '1.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'DECIPHER' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CreateChimeras: no visible binding for global variable 's1'
CreateChimeras: no visible binding for global variable 'd'
CreateChimeras: no visible binding for global variable 'myName'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

DECIPHER.Rcheck/00install.out:


install for i386

* installing *source* package 'DECIPHER' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:273:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterNJ.c:433:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:445:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:192:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:192:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:190:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterUPGMA.c:340:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:352:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:121:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:121:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -shared -s -static-libgcc -o DECIPHER.dll tmp.def Biostrings_stubs.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DECIPHERing.Rnw' 
   'FindChimeras.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'DECIPHER' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:273:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterNJ.c:433:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:445:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:192:41: warning: 'minCol' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:192:33: warning: 'minRow' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:190:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterUPGMA.c:340:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:352:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:121:41: warning: 'minCol' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:121:33: warning: 'minRow' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -m64 -shared -s -static-libgcc -o DECIPHER.dll tmp.def Biostrings_stubs.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_1.0.0.zip

* DONE (DECIPHER)