BAC 1.20.0
Raphael Gottardo
| 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/BAC | | 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/BAC.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 'BAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BAC' version '1.20.0'
* 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 'BAC' can be installed ... [2s/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 ... OK
* checking Rd files ... NOTE
prepare_Rd: BAC.Rd:37-38: Dropping empty section \note
prepare_Rd: CallRegions.Rd:21-23: Dropping empty section \details
prepare_Rd: CallRegions.Rd:34-35: Dropping empty section \note
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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/BAC.Rcheck/BAC/libs/BAC.so':
Found '_printf', possibly from 'printf' (C)
Object: 'BAC.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 ... [153s/155s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
BAC 75.831 0.243 76.895
CallRegions 75.736 0.249 77.175
* 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/BAC.Rcheck/00check.log'
for details.
* installing *source* package 'BAC' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BAC.c -o BAC.o
BAC.c:65:15: warning: implicit conversion from 'double' to 'int' changes value from 0.01 to 0 [-Wliteral-conversion]
w=dvector(*G,0.01);
˜˜˜˜˜˜˜ ^˜˜˜
BAC.c:350:12: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int start=fmax2(0,g-nb_neighbors);
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:238:16: note: expanded from macro 'fmax2'
#define fmax2 Rf_fmax2
^
BAC.c:351:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
int end=fmin2(G-1,g+nb_neighbors);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:239:16: note: expanded from macro 'fmin2'
#define fmin2 Rf_fmin2
^
BAC.c:440:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
start=fmax2(0,g-nb_neighbors);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:238:16: note: expanded from macro 'fmax2'
#define fmax2 Rf_fmax2
^
BAC.c:441:7: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
end=fmin2(G-1,g+nb_neighbors);
˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rmath.h:239:16: note: expanded from macro 'fmin2'
#define fmin2 Rf_fmin2
^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c util.c -o util.o
util.c:77:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
array=(double **)R_alloc(nb_row, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜
util.c:80:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
array[i]=(double *)R_alloc(nb_col, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜
util.c:96:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vector=(double *)R_alloc(length, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜
util.c:113:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
vector=(int *)R_alloc(length, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜
4 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 BAC.so BAC.o util.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BAC.Rcheck/BAC/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BAC)