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Package 209/467HostnameOS / ArchBUILDCHECKBUILD BIN
GraphAlignment 1.14.0
Joern P. Meier
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/GraphAlignment
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GraphAlignment
Version: 1.14.0
Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GraphAlignment_1.14.0.tar.gz
StartedAt: 2011-10-20 15:26:08 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 15:26:33 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 25.5 seconds
RetCode: 0
Status:  OK  
CheckDir: GraphAlignment.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/GraphAlignment.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GraphAlignment/DESCRIPTION' ... OK
* this is package 'GraphAlignment' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GraphAlignment' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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 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

GraphAlignment.Rcheck/00install.out:

* installing *source* package 'GraphAlignment' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c GA_alloc.c -o GA_alloc.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c GA_matrix.c -o GA_matrix.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c GA_matrix_R.c -o GA_matrix_R.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c GA_message.c -o GA_message.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c GA_vector.c -o GA_vector.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c: In function 'GA_clamp_mode_from_R':
GA_vector_R.c:139:9: warning: unused variable 'size'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function 'GA_encode_directed_graph':
GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous 'else'
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous 'else'
GraphAlignment.c: In function 'GA_directed_mode_from_R':
GraphAlignment.c:264:9: warning: unused variable 'size'
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include"          -O3 -Wall  -std=gnu99 -c lap.c -o lap.o
lap.c: In function 'LAP_lap':
lap.c:65:8: warning: 'min' may be used uninitialized in this function
lap.c:64:30: warning: 'last' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o GraphAlignment.dll tmp.def GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/GraphAlignment.Rcheck/GraphAlignment/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GraphAlignment)

GraphAlignment.Rcheck/GraphAlignment-Ex.timings:

nameusersystemelapsed
AlignNetworks0.140.000.14
AlignedPairs0.130.000.13
AnalyzeAlignment0.120.000.12
ComputeLinkParameters0.050.000.05
ComputeM0.060.000.06
ComputeNodeParameters0.020.000.02
ComputeScores0.140.000.14
CreateScoreMatrix000
EncodeDirectedGraph000
GenerateExample000
GetBinNumber000
InitialAlignment000
InvertPermutation000
LinearAssignment000
MatrixToBin000
Permute000
Trace000
VectorToBin000