GeneGroupAnalysis 1.6.0
Alejandro Quiroz-Zarate
| 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/GeneGroupAnalysis | | 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/GeneGroupAnalysis.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 'GeneGroupAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneGroupAnalysis' version '1.6.0'
* 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 'GeneGroupAnalysis' can be installed ... [19s/20s] 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
GeneGrps2AffyGrpsFun: no visible binding for global variable 'GGAdata'
* 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 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [82s/85s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GibbsAllFun.ts 46.821 8.372 57.355
GGAdata 16.501 0.357 17.397
* 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 was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/GeneGroupAnalysis.Rcheck/00check.log'
for details.
* installing *source* package 'GeneGroupAnalysis' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ConditionalsAll.c -o ConditionalsAll.o
In file included from ConditionalsAll.c:8:
In file included from ./InvWishart.h:8:
In file included from ./Densidades.h:8:
In file included from ./OpMat.h:8:
In file included from ./libMatInv.h:8:
./libmat.h:37:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mat=(int*)R_alloc(row,sizeof(int));
˜˜˜˜˜˜˜ ^˜˜
./libmat.h:46:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mat=(double*)R_alloc(row,sizeof(double));
˜˜˜˜˜˜˜ ^˜˜
./libmat.h:55:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ptr1=(double*)R_alloc(row*col,sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜
./libmat.h:56:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mat=(double**)R_alloc(row,sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜
./libmat.h:67:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ptr1=(double*)R_alloc(row*col,sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜^˜˜˜
./libmat.h:68:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mat=(double**)R_alloc(row,sizeof(double*));
˜˜˜˜˜˜˜ ^˜˜
In file included from ConditionalsAll.c:8:
In file included from ./InvWishart.h:8:
In file included from ./Densidades.h:8:
./OpMat.h:20:2: warning: '/*' within block comment [-Wcomment]
/*======================================================
^
./OpMat.h:40:2: warning: '/*' within block comment [-Wcomment]
/*======================================================
^
./OpMat.h:58:2: warning: '/*' within block comment [-Wcomment]
/*======================================================
^
./OpMat.h:76:2: warning: '/*' within block comment [-Wcomment]
/*======================================================
^
./OpMat.h:95:2: warning: '/*' within block comment [-Wcomment]
/*======================================================
^
./OpMat.h:119:2: warning: '/*' within block comment [-Wcomment]
/*======================================================
^
./OpMat.h:153:2: warning: '/*' within block comment [-Wcomment]
/*======================================================
^
./OpMat.h:197:2: warning: '/*' within block comment [-Wcomment]
/*======================================================
^
ConditionalsAll.c:42:3: warning: '/*' within block comment [-Wcomment]
/* Definicion de las variables de trabajo
^
ConditionalsAll.c:152:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
Criwish(vn, TT, AuxLn,RLn);
˜˜˜˜˜˜˜ ^˜
ConditionalsAll.c:193:3: warning: '/*' within block comment [-Wcomment]
/* Definicion de las variables de trabajo
^
ConditionalsAll.c:342:3: warning: '/*' within block comment [-Wcomment]
/* Definicion de las variables de trabajo
^
ConditionalsAll.c:460:3: warning: '/*' within block comment [-Wcomment]
/* Definicion de las variables de trabajo
^
ConditionalsAll.c:646:3: warning: '/*' within block comment [-Wcomment]
/* Definicion de las variables de trabajo
^
20 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 GeneGroupAnalysis.so ConditionalsAll.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GeneGroupAnalysis.Rcheck/GeneGroupAnalysis/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 (GeneGroupAnalysis)