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BioC 2.14: CHECK report for GraphAlignment on morelia

This page was generated on 2014-10-08 09:03:29 -0700 (Wed, 08 Oct 2014).

Package 365/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAlignment 1.28.0
Joern P. Meier
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/GraphAlignment
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: GraphAlignment
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GraphAlignment_1.28.0.tar.gz
StartedAt: 2014-10-07 23:20:09 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:20:28 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 19.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GraphAlignment.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GraphAlignment_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GraphAlignment.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GraphAlignment/DESCRIPTION’ ... OK
* this is package ‘GraphAlignment’ version ‘1.28.0’
* 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 ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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
File ‘GraphAlignment/R/GraphAlignment.R’:
  .Last.lib calls:
    library.dynam.unload("GraphAlignment", libpath)

Package detach functions should not call ‘library.dynam.unload’.
See section ‘Good practice’ in '?.Last.lib'.
* 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 ‘/Users/biocbuild/bbs-2.14-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 entry points 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘GraphAlignment.pdf’ from 417Kb to 311Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/GraphAlignment.Rcheck/00check.log’
for details.

GraphAlignment.Rcheck/00install.out:

* installing *source* package ‘GraphAlignment’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GA_alloc.c -o GA_alloc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GA_matrix.c -o GA_matrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GA_matrix_R.c -o GA_matrix_R.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GA_message.c -o GA_message.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GA_vector.c -o GA_vector.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
    int size = LENGTH(robj);
        ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c:143:23: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                    } else
                      ^
GraphAlignment.c:164:23: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                    } else
                      ^
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
    int size = LENGTH(robj);
        ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c lap.c -o lap.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/GraphAlignment.Rcheck/GraphAlignment/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GraphAlignment)

GraphAlignment.Rcheck/GraphAlignment-Ex.timings:

nameusersystemelapsed
AlignNetworks0.0610.0030.065
AlignedPairs0.0590.0010.060
AnalyzeAlignment0.0560.0010.056
ComputeLinkParameters0.0310.0000.031
ComputeM0.0330.0040.036
ComputeNodeParameters0.0120.0000.012
ComputeScores0.0840.0020.086
CreateScoreMatrix0.0030.0010.004
EncodeDirectedGraph0.0010.0000.001
GenerateExample0.1280.0080.140
GetBinNumber0.0010.0000.001
InitialAlignment0.0020.0000.003
InvertPermutation0.0010.0000.001
LinearAssignment0.0010.0000.001
MatrixToBin0.0010.0000.002
Permute0.0020.0010.003
Trace0.0010.0000.001
VectorToBin0.0010.0000.002