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Package 278/631HostnameOS / ArchBUILDCHECKBUILD BIN
GraphAlignment 1.23.0
Joern P. Meier
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GraphAlignment
Last Changed Rev: 72535 / Revision: 72575
Last Changed Date: 2013-01-15 07:36:22 -0800 (Tue, 15 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / 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 

Summary

Package: GraphAlignment
Version: 1.23.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GraphAlignment_1.23.0.tar.gz
StartedAt: 2013-01-16 03:20:51 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 03:21:08 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 16.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GraphAlignment.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GraphAlignment.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GraphAlignment/DESCRIPTION’ ... OK
* this is package ‘GraphAlignment’ version ‘1.23.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GraphAlignment’ can be installed ... 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GraphAlignment.Rcheck/GraphAlignment/libs/GraphAlignment.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘GA_message.o’, ‘lap.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘lap.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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-2.12-bioc/meat/GraphAlignment.Rcheck/00check.log’
for details.

GraphAlignment.Rcheck/00install.out:

* installing *source* package ‘GraphAlignment’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GA_alloc.c -o GA_alloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GA_matrix.c -o GA_matrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GA_matrix_R.c -o GA_matrix_R.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GA_message.c -o GA_message.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GA_vector.c -o GA_vector.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GA_vector_R.c -o GA_vector_R.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GraphAlignment.c -o GraphAlignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c lap.c -o lap.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o GraphAlignment.so GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/GraphAlignment.Rcheck/GraphAlignment/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GraphAlignment.Rnw’ 
** testing if installed package can be loaded

* DONE (GraphAlignment)

GraphAlignment.Rcheck/GraphAlignment-Ex.timings:

nameusersystemelapsed
AlignNetworks0.1080.0040.112
AlignedPairs0.1040.0000.106
AnalyzeAlignment0.1120.0000.112
ComputeLinkParameters0.0360.0000.039
ComputeM0.0600.0040.063
ComputeNodeParameters0.0240.0000.023
ComputeScores0.1840.0000.184
CreateScoreMatrix0.0080.0000.007
EncodeDirectedGraph0.0040.0000.003
GenerateExample0.1720.0000.173
GetBinNumber0.0040.0000.004
InitialAlignment0.0040.0000.006
InvertPermutation0.0040.0000.003
LinearAssignment0.0040.0000.003
MatrixToBin0.0040.0000.005
Permute0.0040.0000.006
Trace0.0040.0000.003
VectorToBin0.0040.0000.004