BioC 2.11: CHECK report for MotIV on lamb1

Package: MotIV

Version: 1.14.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings MotIV_1.14.0.tar.gz

StartedAt: 2013-03-25 03:13:55 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:17:27 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 211.3 seconds

RetCode: 0

Status: OK

CheckDir: MotIV.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/MotIV.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.14.0’
* 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 ‘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 ... OK
* checking top-level files ... OK
* checking for left-over 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
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 ... 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 ... 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/MotIV.Rcheck/00check.log’
for details.

* installing *source* package ‘MotIV’ ...
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Alignment.cpp -o Alignment.o
Alignment.cpp: In member function ‘double Alignment::AlignMotifs2D(Motif*, Motif*, int&, int&, int&, bool&, bool&)’:
Alignment.cpp:176:17: warning: unused variable ‘score2’ [-Wunused-variable]
Alignment.cpp:177:18: warning: unused variable ‘i1_B’ [-Wunused-variable]
Alignment.cpp:177:24: warning: unused variable ‘i2_B’ [-Wunused-variable]
Alignment.cpp:178:12: warning: unused variable ‘aL_B’ [-Wunused-variable]
Alignment.cpp:179:14: warning: unused variable ‘for_B’ [-Wunused-variable]
Alignment.cpp:184:9: warning: variable ‘currOne’ set but not used [-Wunused-but-set-variable]
Alignment.cpp:185:9: warning: unused variable ‘currTwo’ [-Wunused-variable]
Alignment.cpp: In member function ‘virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:423:9: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable]
Alignment.cpp: In member function ‘virtual double SmithWatermanAffine::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:883:2: warning: ‘forScore’ may be used uninitialized in this function [-Wuninitialized]
Alignment.cpp: In member function ‘virtual double NeedlemanWunsch::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:713:2: warning: ‘forScore’ may be used uninitialized in this function [-Wuninitialized]
Alignment.cpp: In member function ‘virtual double SmithWaterman::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:319:2: warning: ‘revScore’ may be used uninitialized in this function [-Wuninitialized]
Alignment.cpp:319:2: warning: ‘forScore’ may be used uninitialized in this function [-Wuninitialized]
Alignment.cpp: In member function ‘virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:491:2: warning: ‘forScore’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c ColumnComp.cpp -o ColumnComp.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c DeclareAll.cpp -o DeclareAll.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Motif.cpp -o Motif.o
Motif.cpp: In member function ‘char Motif::ColConsensus(int)’:
Motif.cpp:148:7: warning: variable ‘three_base_l’ set but not used [-Wunused-but-set-variable]
Motif.cpp:149:9: warning: variable ‘three_base_c’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp: In function ‘SEXPREC* motifDistances(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
MotifDistances.cpp:50:10: warning: variable ‘colChosen’ set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:50:27: warning: variable ‘alignChosen’ set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:51:6: warning: variable ‘matchTopX’ set but not used [-Wunused-but-set-variable]
MotifDistances.cpp:58:7: warning: variable ‘ungapped’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp: In function ‘SEXPREC* motifMatch(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
MotifMatch.cpp:50:10: warning: variable ‘colChosen’ set but not used [-Wunused-but-set-variable]
MotifMatch.cpp:50:27: warning: variable ‘alignChosen’ set but not used [-Wunused-but-set-variable]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp: In member function ‘void PlatformSupport::PreAlign(Alignment*)’:
PlatformSupport.cpp:412:47: warning: variable ‘max_score’ set but not used [-Wunused-but-set-variable]
PlatformSupport.cpp: In member function ‘int PlatformSupport::ReadTransfacFile(SEXP, SEXP)’:
PlatformSupport.cpp:127:27: warning: ‘input’ may be used uninitialized in this function [-Wuninitialized]
PlatformSupport.cpp:141:34: warning: ‘currMotifs’ may be used uninitialized in this function [-Wuninitialized]
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp: In function ‘SEXPREC* generateScoresDB(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
generateScoresDB.cpp:54:10: warning: variable ‘colChosen’ set but not used [-Wunused-but-set-variable]
generateScoresDB.cpp:54:27: warning: variable ‘alignChosen’ set but not used [-Wunused-but-set-variable]
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-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/MotIV.Rcheck/MotIV/libs
** R
** data
** inst
** preparing package for lazy loading
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
** installing vignettes
   ‘MotIV.Rnw’ using ‘latin1’ 
** testing if installed package can be loaded

* DONE (MotIV)

name	user	system	elapsed
FOXA_rGADEM	1.292	0.020	1.329
as.data.frame	0.844	0.028	0.902
combineMotifs	0.824	0.012	0.837
exportAsRangedData	4.756	0.012	4.849
exportAsTransfacFile	0.492	0.004	0.498
filter-class	0.000	0.000	0.001
filter-methods	0	0	0
filter	0.504	0.012	0.515
generateDBScores	0.028	0.000	0.027
getGademPWM	0.216	0.004	0.219
jaspar	0.832	0.008	0.838
makePWM	0	0	0
matches-class	0.000	0.000	0.001
motifDistance	0.457	0.008	0.487
motifMatch	0.444	0.000	0.458
motifOccurences	2.960	0.000	2.996
motiv-class	0.000	0.004	0.000
motiv-methods	0	0	0
plot	4.504	0.016	4.593
readGademPWMFile	0.204	0.004	0.209
readPWMfile	0.024	0.000	0.023
seqLogo2	0	0	0
setFilter	0.516	0.000	0.522
split	0.468	0.000	0.482
tf-class	0.000	0.000	0.001
trimPWMedge	0.508	0.004	0.511
viewAlignment	0.448	0.004	0.502
viewMotifs	0.420	0.008	0.452

Summary

Command output