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Package 421/658HostnameOS / ArchBUILDCHECKBUILD BIN
MotIV 1.15.1
Eloi Mercier , Raphael Gottardo
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MotIV
Last Changed Rev: 72298 / Revision: 74756
Last Changed Date: 2013-01-04 13:18:09 -0800 (Fri, 04 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: MotIV
Version: 1.15.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MotIV_1.15.1.tar.gz
StartedAt: 2013-03-24 08:01:11 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 08:05:26 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 254.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MotIV.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MotIV.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MotIV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MotIV' version '1.15.1'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'MotIV' can be installed ... [24s/27s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... [42s/47s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plot               7.470  0.089   8.518
motifOccurences    6.530  0.065   7.439
exportAsRangedData 5.485  0.076   6.287
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/MotIV.Rcheck/00check.log'
for details.

MotIV.Rcheck/00install.out:

* installing *source* package 'MotIV' ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking for gsl-config... /usr/local/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Alignment.cpp -o Alignment.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c ColumnComp.cpp -o ColumnComp.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c DeclareAll.cpp -o DeclareAll.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Motif.cpp -o Motif.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c MotifDistances.cpp -o MotifDistances.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c MotifMatch.cpp -o MotifMatch.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c PlatformSupport.cpp -o PlatformSupport.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c RandPSSMGen.cpp -o RandPSSMGen.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c generateScoresDB.cpp -o generateScoresDB.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MotIV.so Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-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)

MotIV.Rcheck/MotIV-Ex.timings:

nameusersystemelapsed
FOXA_rGADEM1.3270.0521.508
as.data.frame1.1230.0451.338
combineMotifs0.7660.0270.868
exportAsRangedData5.4850.0766.287
exportAsTransfacFile1.0970.0231.252
filter-class0.0080.0030.010
filter-methods0.0080.0030.010
filter0.7480.0220.869
generateDBScores0.0590.0040.067
getGademPWM0.3950.0170.457
jaspar1.0660.0251.237
makePWM0.0130.0020.016
matches-class0.0110.0040.015
motifDistance0.8040.0211.019
motifMatch1.0820.0221.179
motifOccurences6.5300.0657.439
motiv-class0.0070.0020.009
motiv-methods0.0120.0030.023
plot7.4700.0898.518
readGademPWMFile0.3680.0210.447
readPWMfile0.0630.0020.075
seqLogo20.0240.0020.027
setFilter0.7580.0270.903
split0.7950.0190.821
tf-class0.0140.0010.016
trimPWMedge0.3690.0140.385
viewAlignment0.7440.0250.772
viewMotifs0.6960.0170.714