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Package 156/419HostnameOS / ArchBUILDCHECKBUILD BIN
GeneR 2.20.0
Y. d'Aubenton-Carafa
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/GeneR
Last Changed Rev: 50293 / Revision: 54588
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  ERROR 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 

Summary

Package: GeneR
Version: 2.20.0
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneR_2.20.0.tar.gz
StartedAt: 2011-04-07 07:05:27 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 07:06:18 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 50.4 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneR.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/GeneR.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '2.20.0'
* 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 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
* 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
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c GeneR_glob.cc -o GeneR_glob.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c GeneR_seq.cc -o GeneR_seq.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c complementaire.cc -o complementaire.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c compoSeq.cc -o compoSeq.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c dnaRna.cc -o dnaRna.o
dnaRna.cc: In function 'void dna_rna(int*, int*, int*, int*, int*)':
dnaRna.cc:62:15: warning: value computed is not used
dnaRna.cc:63:13: warning: value computed is not used
dnaRna.cc: In function 'void rna_dna(int*, int*, int*, int*, int*)':
dnaRna.cc:108:15: warning: value computed is not used
dnaRna.cc:109:13: warning: value computed is not used
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c libIndex.cc -o libIndex.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c libStrings.cc -o libStrings.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c makeIndex.cc -o makeIndex.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c masked.cc -o masked.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c misc.cc -o misc.o
misc.cc: In function 'SEXPREC* str_to_nbstr(SEXPREC*, SEXPREC*)':
misc.cc:31:18: warning: 'multiple' may be used uninitialized in this function
misc.cc:30:8: warning: 'ans' may be used uninitialized in this function
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c readEmblDescript.cc -o readEmblDescript.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c readIndex.cc -o readIndex.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c readLocation.cc -o readLocation.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c readSeqFasta.cc -o readSeqFasta.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c readSeqGbk.cc -o readSeqGbk.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c seqManip.cc -o seqManip.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O3 -Wall  -std=gnu99 -c strcasestr.c -o strcasestr.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c translate.cc -o translate.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c upperSeq.cc -o upperSeq.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c vecteurs.cc -o vecteurs.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include"         -O2 -Wall  -c writeFasta.cc -o writeFasta.o
g++ -shared -s -static-libgcc -o GeneR.dll tmp.def 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 -LE:/biocbld/BBS-2˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-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
01GeneR0.210.034.71
02globalSeg0.090.000.09
02globals0.020.000.02
Allorf0.010.000.01
AtoR000
Match0.020.000.02
Xor.globalSeg0.120.000.12
Xor.segSet0.020.000.02
and.globalSeg0.060.000.06
and.segSet0.020.000.02
appendSeq000
assemble000
bankDensityProfile0.160.020.19
bankSummary0.190.010.22
compos.seq000
concat000
deleteCR000
densityProfile0.240.000.24
dna.rna000
exact.word000
fasta.descript000
free.seq0.020.000.02
getseq000
insert000
lower000
makeIndex000
mask000
not.globalSeg0.110.000.13
not.segSet0.020.000.01
or.globalSeg0.010.000.02
or.segSet000
placestring000
plot.globalSeg0.020.000.01
posMaskedSeq000
randomSeq000
read.gbk.location000
readEmblDescript000
readseq000
relist0.020.000.01
revcomp000
seqSkew0.020.000.02
sequrl000
size.globalSeg000
sizeseq0.030.000.03
sizeseqfasta000
sliceSegment0.010.000.02
translation000
write.fasta0.020.000.01
writeEMBL0.010.000.02