GraphAlignment 1.24.0
Joern P. Meier
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GraphAlignment | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 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 Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GraphAlignment.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GraphAlignment/DESCRIPTION' ... OK
* this is package 'GraphAlignment' version '1.24.0'
* 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 ... [3s/3s] 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/GraphAlignment.so':
Found '_printf', possibly from 'printf' (C)
Objects: 'GA_message.o', '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 installed files from 'inst/doc' ... OK
* checking examples ... [2s/3s] 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 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/GraphAlignment.Rcheck/00check.log'
for details.
* installing *source* package 'GraphAlignment' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c GA_alloc.c -o GA_alloc.o
GA_alloc.c:57:5: warning: void function 'GA_free' should not return void expression [-Wpedantic]
return GA_FREE_FUNC(memLoc);
^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c GA_matrix.c -o GA_matrix.o
GA_matrix.c:50:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matrix->elts = (int**)GA_alloc(rows, sizeof(int*));
˜˜˜˜˜˜˜˜ ^˜˜˜
GA_matrix.c:61:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matrix->elts[i] = (int*)GA_alloc(cols, sizeof(int));
˜˜˜˜˜˜˜˜ ^˜˜˜
GA_matrix.c:211:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matrix->elts = (double**)GA_alloc(rows, sizeof(double*));
˜˜˜˜˜˜˜˜ ^˜˜˜
GA_matrix.c:222:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matrix->elts[i] = (double*)GA_alloc(cols, sizeof(double));
˜˜˜˜˜˜˜˜ ^˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c GA_matrix_R.c -o GA_matrix_R.o
GA_matrix_R.c:39:27: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE matrixType = TYPEOF(robj);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
GA_matrix_R.c:94:27: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE matrixType = TYPEOF(robj);
˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c GA_message.c -o GA_message.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c GA_vector.c -o GA_vector.o
GA_vector.c:49:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vec->elts = (int*)GA_alloc(size, sizeof(int));
˜˜˜˜˜˜˜˜ ^˜˜˜
GA_vector.c:157:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vec->elts = (double*)GA_alloc(size, sizeof(double));
˜˜˜˜˜˜˜˜ ^˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c:39:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE vecType = TYPEOF(robj);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
GA_vector_R.c:82:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE vecType = TYPEOF(robj);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
GA_vector_R.c:125:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE objType = TYPEOF(robj);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
int size = LENGTH(robj);
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -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:250:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
SEXPTYPE objType = TYPEOF(robj);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
int size = LENGTH(robj);
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c lap.c -o lap.o
lap.c:67:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
rfree = (row*)GA_alloc(dim, sizeof(row));
˜˜˜˜˜˜˜˜ ^˜˜
lap.c:68:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
collist = (col*)GA_alloc(dim, sizeof(col));
˜˜˜˜˜˜˜˜ ^˜˜
lap.c:69:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matches = (col*)GA_alloc(dim, sizeof(col));
˜˜˜˜˜˜˜˜ ^˜˜
lap.c:70:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
d = (cost*)GA_alloc(dim, sizeof(cost));
˜˜˜˜˜˜˜˜ ^˜˜
lap.c:71:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pred = (row*)GA_alloc(dim, sizeof(row));
˜˜˜˜˜˜˜˜ ^˜˜
lap.c:339:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
matched = (boolean*)GA_alloc(dim, sizeof(boolean));
˜˜˜˜˜˜˜˜ ^˜˜
6 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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
** 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)