Package: MotIV

Version: 1.4.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings MotIV_1.4.0.tar.gz

StartedAt: 2011-04-07 07:49:48 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 07:52:08 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 139.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MotIV.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/MotIV.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MotIV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotIV’ version ‘1.4.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘MotIV’ can be installed ... 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
plot,motiv-ANY: no visible binding for global variable ‘y’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  gadem
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... 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 examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/MotIV.Rcheck/00check.log’
for details

* installing *source* package ‘MotIV’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Alignment.cpp -o Alignment.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ColumnComp.cpp -o ColumnComp.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c DeclareAll.cpp -o DeclareAll.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Motif.cpp -o Motif.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c MotifDistances.cpp -o MotifDistances.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c MotifMatch.cpp -o MotifMatch.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c PlatformSupport.cpp -o PlatformSupport.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c generateScoresDB.cpp -o generateScoresDB.o
g++ -shared -L/usr/local/lib64 -o MotIV.so Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/MotIV.Rcheck/MotIV/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "MotIV"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (MotIV)

name	user	system	elapsed
combine	0.780	0.024	0.801
exportAsRangedData	4.252	0.032	4.284
exportAsTransfacFile	0.320	0.008	0.329
filter-class	0.000	0.000	0.001
filter-methods	0	0	0
filter	0.352	0.004	0.357
generateDBScores	0.044	0.004	0.047
getGademPWM	0.160	0.004	0.164
jaspar	0.264	0.004	0.266
makePWM	0	0	0
matches-class	0.000	0.000	0.001
motifDistance	0.328	0.000	0.327
motifMatch	0.308	0.004	0.311
motifOccurences	2.616	0.004	2.619
motiv-class	0.000	0.000	0.001
motiv-methods	0.004	0.000	0.001
plot	3.981	0.048	4.029
readGademPWMFile	0.156	0.004	0.161
readPWMfile	0.04	0.00	0.04
seqLogo	0	0	0
setFilter	0.324	0.004	0.326
split	0.316	0.008	0.324
tf-class	0	0	0
trimPWMedge	0.156	0.004	0.162
viewAlignment	0.320	0.000	0.318
viewMotifs	0.300	0.000	0.298