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Package 176/462HostnameOS / ArchBUILDCHECKBUILD BIN
GeneR 2.23.0
Y. d'Aubenton-Carafa
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneR
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 

Summary

Package: GeneR
Version: 2.23.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings GeneR_2.23.0.tar.gz
StartedAt: 2011-05-09 13:38:27 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 13:39:14 -0700 (Mon, 09 May 2011)
EllapsedTime: 47.0 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneR.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/GeneR.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '2.23.0'
* 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 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 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

GeneR.Rcheck/00install.out:

* installing *source* package 'GeneR' ...
** libs
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c GeneR_glob.cc -o GeneR_glob.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c GeneR_seq.cc -o GeneR_seq.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c complementaire.cc -o complementaire.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c compoSeq.cc -o compoSeq.o
g++  -I"E:/biocbld/BBS-2˜1.9-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˜1.9-B/R/include"          -O2 -Wall  -c libIndex.cc -o libIndex.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c libStrings.cc -o libStrings.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c makeIndex.cc -o makeIndex.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c masked.cc -o masked.o
g++  -I"E:/biocbld/BBS-2˜1.9-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˜1.9-B/R/include"          -O2 -Wall  -c readEmblDescript.cc -o readEmblDescript.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c readIndex.cc -o readIndex.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c readLocation.cc -o readLocation.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c readSeqEmbl.cc -o readSeqEmbl.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c readSeqFasta.cc -o readSeqFasta.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c readSeqGbk.cc -o readSeqGbk.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c seqManip.cc -o seqManip.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c strcasestr.c -o strcasestr.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c translate.cc -o translate.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c upperSeq.cc -o upperSeq.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O2 -Wall  -c vecteurs.cc -o vecteurs.o
g++  -I"E:/biocbld/BBS-2˜1.9-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˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GeneR.Rnw' 
** testing if installed package can be loaded

* DONE (GeneR)

GeneR.Rcheck/GeneR-Ex.timings:

nameusersystemelapsed
01GeneR0.140.020.64
02globalSeg0.070.000.08
02globals000
Allorf0.040.000.03
AtoR000
Match000
Xor.globalSeg0.070.000.07
Xor.segSet000
and.globalSeg0.050.000.05
and.segSet0.020.000.02
appendSeq000
assemble000
bankDensityProfile0.140.010.22
bankSummary0.150.000.17
compos.seq000
concat000
deleteCR0.020.000.29
densityProfile0.140.020.16
dna.rna000
exact.word000
fasta.descript0.000.000.19
free.seq0.010.000.01
getseq000
insert000
lower000
makeIndex0.000.000.18
mask000
not.globalSeg0.060.000.06
not.segSet0.020.000.02
or.globalSeg0.010.000.02
or.segSet000
placestring000
plot.globalSeg000
posMaskedSeq0.040.000.03
randomSeq0.000.000.32
read.gbk.location0.000.010.02
readEmblDescript000
readseq0.010.020.38
relist000
revcomp000
seqSkew0.020.000.01
sequrl0.000.000.28
size.globalSeg000
sizeseq000
sizeseqfasta0.060.002.02
sliceSegment000
translation000
write.fasta0.010.000.01
writeEMBL0.000.010.02