Package: MotIV

Version: 1.8.1

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings MotIV_1.8.1.tar.gz

StartedAt: 2012-03-24 01:36:38 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:39:20 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 161.9 seconds

RetCode: 0

Status:  OK

CheckDir: MotIV.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/MotIV.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 ‘MotIV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotIV’ version ‘1.8.1’
* 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 ‘MotIV’ 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:
  GPL 2
Standardizable: TRUE
Standardized license specification:
  GPL-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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                   old_size new_size compress
  FOXA1_rGADEM.rda    297Kb    153Kb       xz
* 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 compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/MotIV.Rcheck/MotIV/libs/MotIV.so’:
  Found ‘exit’, possibly from ‘exit’ (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

* 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-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Alignment.cpp -o Alignment.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c ColumnComp.cpp -o ColumnComp.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c DeclareAll.cpp -o DeclareAll.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Motif.cpp -o Motif.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c MotifDistances.cpp -o MotifDistances.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c MotifMatch.cpp -o MotifMatch.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c PlatformSupport.cpp -o PlatformSupport.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -I/home/biocbuild/bbs-2.9-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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/MotIV.Rcheck/MotIV/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for class “pwm” in package ‘MotIV’ seems equivalent to one from package ‘seqLogo’ and is not turning on duplicate class definitions for this class
Creating a new generic function for ‘filter’ in package ‘MotIV’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘MotIV’
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘MotIV.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded

* DONE (MotIV)

name	user	system	elapsed
FOXA_rGADEM	0.548	0.012	0.559
combineMotifs	0.560	0.012	0.572
exportAsRangedData	4.444	0.024	4.469
exportAsTransfacFile	0.312	0.020	0.331
filter-class	0.000	0.000	0.001
filter-methods	0.000	0.000	0.001
filter	0.352	0.000	0.355
generateDBScores	0.052	0.000	0.053
getGademPWM	0.160	0.004	0.162
jaspar	0.268	0.000	0.269
makePWM	0	0	0
matches-class	0	0	0
motifDistance	0.340	0.008	0.349
motifMatch	0.292	0.000	0.292
motifOccurences	2.884	0.008	2.897
motiv-class	0	0	0
motiv-methods	0.000	0.000	0.001
plot	4.389	0.048	4.462
readGademPWMFile	0.176	0.004	0.199
readPWMfile	0.048	0.004	0.056
seqLogo	0	0	0
setFilter	0.356	0.008	0.378
split	0.388	0.000	0.391
tf-class	0.000	0.000	0.001
trimPWMedge	0.172	0.000	0.171
viewAlignment	0.324	0.004	0.329
viewMotifs	0.328	0.008	0.342