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Package 162/444HostnameOS / ArchBUILDCHECKBUILD BIN
GeneR 2.21.0
Y. d'Aubenton-Carafa
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneR
Last Changed Rev: 50295 / Revision: 53825
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ OK ] OK 

Summary

Package: GeneR
Version: 2.21.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneR_2.21.0.tar.gz
StartedAt: 2011-03-17 16:23:08 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 16:23:46 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 38.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/GeneR.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.21.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GeneR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
and.segSet: possible error in as.segSet(deb, fin): unused argument(s)
  (fin)
relist: no visible global function definition for 'error'
setParam: no visible global function definition for 'seqSize'
* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

GeneR.Rcheck/00install.out:

* installing *source* package 'GeneR' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c GeneR_glob.cc -o GeneR_glob.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c GeneR_seq.cc -o GeneR_seq.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c complementaire.cc -o complementaire.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c compoSeq.cc -o compoSeq.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c dnaRna.cc -o dnaRna.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c libIndex.cc -o libIndex.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c libStrings.cc -o libStrings.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c makeIndex.cc -o makeIndex.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c masked.cc -o masked.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c misc.cc -o misc.o
misc.cc: In function 'SEXPREC* str_to_nbstr(SEXPREC*, SEXPREC*)':
misc.cc:31: warning: 'multiple' may be used uninitialized in this function
misc.cc:30: warning: 'ans' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readEmblDescript.cc -o readEmblDescript.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readIndex.cc -o readIndex.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readLocation.cc -o readLocation.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readSeqFasta.cc -o readSeqFasta.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c readSeqGbk.cc -o readSeqGbk.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c seqManip.cc -o seqManip.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c strcasestr.c -o strcasestr.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c translate.cc -o translate.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c upperSeq.cc -o upperSeq.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c vecteurs.cc -o vecteurs.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c writeFasta.cc -o writeFasta.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneR.so GeneR_glob.o GeneR_seq.o complementaire.o compoSeq.o dnaRna.o libIndex.o libStrings.o makeIndex.o masked.o misc.o readEmblDescript.o readIndex.o readLocation.o readSeqEmbl.o readSeqFasta.o readSeqGbk.o seqManip.o strcasestr.o translate.o upperSeq.o vecteurs.o writeFasta.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/GeneR.Rcheck/GeneR/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GeneR)

GeneR.Rcheck/GeneR-Ex.timings:

nameusersystemelapsed
01GeneR0.1440.0132.325
02globalSeg0.0700.0010.071
02globals0.0070.0020.010
Allorf0.0280.0000.028
AtoR0.0010.0000.001
Match0.0040.0010.005
Xor.globalSeg0.0830.0010.084
Xor.segSet0.0100.0010.011
and.globalSeg0.0440.0010.045
and.segSet0.0090.0010.010
appendSeq0.0000.0000.001
assemble0.0040.0010.004
bankDensityProfile0.1280.0110.144
bankSummary0.1290.0270.173
compos.seq0.0050.0010.006
concat0.0010.0000.002
deleteCR000
densityProfile0.1640.0050.169
dna.rna0.0020.0000.002
exact.word0.0040.0010.004
fasta.descript000
free.seq0.0160.0030.020
getseq0.0010.0000.001
insert000
lower0.0040.0010.004
makeIndex000
mask0.0010.0010.001
not.globalSeg0.0870.0010.088
not.segSet0.0100.0000.012
or.globalSeg0.0110.0000.012
or.segSet0.0050.0010.004
placestring0.0010.0000.001
plot.globalSeg0.0010.0010.002
posMaskedSeq0.0080.0020.011
randomSeq0.0020.0000.002
read.gbk.location0.0000.0010.001
readEmblDescript000
readseq0.0020.0010.002
relist0.0060.0000.006
revcomp0.0030.0010.003
seqSkew0.0050.0000.005
sequrl0.0000.0010.000
size.globalSeg0.0030.0000.003
sizeseq0.0200.0010.021
sizeseqfasta0.0000.0000.001
sliceSegment0.0030.0010.003
translation0.0050.0020.007
write.fasta0.0040.0010.005
writeEMBL0.0220.0020.024