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Package 196/514HostnameOS / ArchBUILDCHECKBUILD BIN
GeneR 2.24.0
Y. d'Aubenton-Carafa
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/GeneR
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  ERROR  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GeneR
Version: 2.24.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings GeneR_2.24.0.tar.gz
StartedAt: 2012-03-24 00:31:51 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:32:27 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 35.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneR/DESCRIPTION’ ... OK
* this is package ‘GeneR’ version ‘2.24.0’
* 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 ‘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 ... NOTE
Non-standard license specification:
  CeCILL-2.0
Standardizable: TRUE
Standardized license specification:
  CeCILL-2
* 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 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
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 ... NOTE
S3 methods shown with full name in documentation object 'Xor.globalSeg':
  ‘Xor.globalSeg’

S3 methods shown with full name in documentation object 'Xor.segSet':
  ‘Xor.segSet’

S3 methods shown with full name in documentation object 'and.globalSeg':
  ‘and.globalSeg’

S3 methods shown with full name in documentation object 'and.segSet':
  ‘and.segSet’

S3 methods shown with full name in documentation object 'as.globalSeg':
  ‘as.matrix.globalSeg’ ‘range.globalSeg’

S3 methods shown with full name in documentation object 'as.segSet':
  ‘as.matrix.segSet’ ‘as.data.frame.segSet’ ‘plot.segSet’

S3 methods shown with full name in documentation object 'densityProfile':
  ‘plot.profile’

S3 methods shown with full name in documentation object 'not.globalSeg':
  ‘not.globalSeg’

S3 methods shown with full name in documentation object 'not.segSet':
  ‘not.segSet’

S3 methods shown with full name in documentation object 'or.globalSeg':
  ‘or.globalSeg’

S3 methods shown with full name in documentation object 'or.segSet':
  ‘or.segSet’

S3 methods shown with full name in documentation object 'plot.globalSeg':
  ‘plot.globalSeg’

S3 methods shown with full name in documentation object 'size.globalSeg':
  ‘size.globalSeg’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs/GeneR.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c GeneR_glob.cc -o GeneR_glob.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c GeneR_seq.cc -o GeneR_seq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c complementaire.cc -o complementaire.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c compoSeq.cc -o compoSeq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c dnaRna.cc -o dnaRna.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c libIndex.cc -o libIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c libStrings.cc -o libStrings.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c makeIndex.cc -o makeIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c masked.cc -o masked.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c misc.cc -o misc.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readEmblDescript.cc -o readEmblDescript.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readIndex.cc -o readIndex.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readLocation.cc -o readLocation.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqEmbl.cc -o readSeqEmbl.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqFasta.cc -o readSeqFasta.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c readSeqGbk.cc -o readSeqGbk.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c seqManip.cc -o seqManip.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c strcasestr.c -o strcasestr.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c translate.cc -o translate.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c upperSeq.cc -o upperSeq.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c vecteurs.cc -o vecteurs.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c writeFasta.cc -o writeFasta.o
g++ -shared -L/usr/local/lib64 -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 -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/GeneR.Rcheck/GeneR/libs
** 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
01GeneR0.0920.0080.422
02globalSeg0.0880.0000.088
02globals0.0120.0040.010
Allorf0.0320.0000.031
AtoR000
Match0.0040.0000.007
Xor.globalSeg0.0840.0000.086
Xor.segSet0.0080.0000.010
and.globalSeg0.0520.0000.055
and.segSet0.0080.0040.014
appendSeq000
assemble0.0080.0000.006
bankDensityProfile0.1080.0000.112
bankSummary0.0600.0040.068
compos.seq0.0040.0040.006
concat0.0000.0000.001
deleteCR0.0040.0040.317
densityProfile0.1600.0000.159
dna.rna0.0040.0000.001
exact.word0.0040.0000.002
fasta.descript0.0080.0000.252
free.seq0.0200.0040.022
getseq0.0000.0040.001
insert000
lower0.0080.0000.005
makeIndex0.0080.0000.317
mask0.0000.0000.001
not.globalSeg0.1280.0160.221
not.segSet0.0120.0000.016
or.globalSeg0.0080.0000.015
or.segSet0.0080.0000.008
placestring0.0000.0000.001
plot.globalSeg0.0040.0000.002
posMaskedSeq0.0080.0000.009
randomSeq0.0160.0000.278
read.gbk.location000
readEmblDescript0.0000.0000.001
readseq0.0320.0000.357
relist0.0040.0000.010
revcomp0.0080.0000.006
seqSkew0.0000.0040.006
sequrl0.0040.0000.415
size.globalSeg0.0040.0000.004
sizeseq0.0080.0000.006
sizeseqfasta0.0200.0040.933
sliceSegment0.0000.0000.002
translation0.0040.0040.006
write.fasta0.0040.0000.005
writeEMBL0.0200.0040.022