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Package 308/479HostnameOS / ArchBUILDCHECKBUILD BIN
MotIV 1.7.0
Eloi Mercier , Raphael Gottardo
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotIV
Last Changed Rev: 56153 / Revision: 56603
Last Changed Date: 2011-06-13 15:40:41 -0700 (Mon, 13 Jun 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  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  ERROR 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: MotIV
Version: 1.7.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings MotIV_1.7.0.tar.gz
StartedAt: 2011-07-07 01:32:18 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 01:34:50 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 151.4 seconds
RetCode: 0
Status:  OK 
CheckDir: MotIV.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/MotIV.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.7.0’
* 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 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 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 ... 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 ... 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 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

MotIV.Rcheck/00install.out:

* 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 -Wall -c Alignment.cpp -o Alignment.o
Alignment.cpp: In member function ‘virtual double SmithWatermanAffine::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:793:9: warning: ‘forScore’ may be used uninitialized in this function
Alignment.cpp: In member function ‘virtual double NeedlemanWunsch::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:592:9: warning: ‘forScore’ may be used uninitialized in this function
Alignment.cpp: In member function ‘virtual double SmithWaterman::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:244:9: warning: ‘forScore’ may be used uninitialized in this function
Alignment.cpp:244:19: warning: ‘revScore’ may be used uninitialized in this function
Alignment.cpp: In member function ‘virtual double SmithWatermanUngappedExtended::AlignMotifs(Motif*, Motif*, int&, int&, int&, bool&)’:
Alignment.cpp:426:9: warning: ‘forScore’ may be used uninitialized in this function
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c ColumnComp.cpp -o ColumnComp.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c DeclareAll.cpp -o DeclareAll.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Motif.cpp -o Motif.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c MotifDistances.cpp -o MotifDistances.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c MotifMatch.cpp -o MotifMatch.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c PlatformSupport.cpp -o PlatformSupport.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c RandPSSMGen.cpp -o RandPSSMGen.o
g++ -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -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
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)

MotIV.Rcheck/MotIV-Ex.timings:

nameusersystemelapsed
FOXA_rGADEM0.8440.0040.882
combineMotifs0.6600.0320.733
exportAsRangedData4.9680.0285.008
exportAsTransfacFile0.4120.0040.418
filter-class0.0000.0000.001
filter-methods0.0000.0000.001
filter0.6840.0040.688
generateDBScores0.0440.0040.048
getGademPWM0.1920.0040.196
jaspar0.2960.0040.303
makePWM000
matches-class0.0000.0000.001
motifDistance0.3720.0000.371
motifMatch0.3480.0080.358
motifOccurences2.7850.0002.785
motiv-class0.0000.0000.001
motiv-methods000
plot5.0360.0405.087
readGademPWMFile0.1760.0080.185
readPWMfile0.0600.0000.058
seqLogo000
setFilter0.4000.0040.402
split0.7040.0000.709
tf-class000
trimPWMedge0.1760.0000.179
viewAlignment0.3640.0040.369
viewMotifs0.3640.0000.362