GraphAlignment 1.23.1
Joern P. Meier
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GraphAlignment | | Last Changed Rev: 73901 / Revision: 74774 | | Last Changed Date: 2013-03-04 13:42:29 -0800 (Mon, 04 Mar 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 |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GraphAlignment.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GraphAlignment/DESCRIPTION' ... OK
* this is package 'GraphAlignment' version '1.23.1'
* 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 'GraphAlignment' can be installed ... [3s/4s] 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
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-2.12-bioc/meat/GraphAlignment.Rcheck/GraphAlignment/libs/i386/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 examples ... [2s/2s] 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 were 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/GraphAlignment.Rcheck/00check.log'
for details.
* installing *source* package 'GraphAlignment' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c GA_alloc.c -o GA_alloc.o
GA_alloc.c: In function 'GA_free':
GA_alloc.c:57: warning: 'return' with a value, in function returning void
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c GA_matrix.c -o GA_matrix.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c GA_matrix_R.c -o GA_matrix_R.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c GA_message.c -o GA_message.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c GA_vector.c -o GA_vector.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -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: warning: unused variable 'size'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function 'GA_encode_directed_graph':
GraphAlignment.c:138: warning: suggest explicit braces to avoid ambiguous 'else'
GraphAlignment.c:159: warning: suggest explicit braces to avoid ambiguous 'else'
GraphAlignment.c: In function 'GA_directed_mode_from_R':
GraphAlignment.c:264: warning: unused variable 'size'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c lap.c -o lap.o
lap.c: In function 'LAP_lap':
lap.c:65: warning: 'min' may be used uninitialized in this function
lap.c:64: warning: 'last' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -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-2.12-bioc/meat/GraphAlignment.Rcheck/GraphAlignment/libs/i386
** 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)