GlobalAncova 3.28.0
Manuela Hummel
| 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/GlobalAncova | | 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/GlobalAncova.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 'GlobalAncova/DESCRIPTION' ... OK
* this is package 'GlobalAncova' version '3.28.0'
* 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 'GlobalAncova' can be installed ... [17s/17s] 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 'GlobalAncova/R/zzz.r':
.onLoad calls:
require(methods)
Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/GlobalAncova.Rcheck/GlobalAncova/libs/GlobalAncova.so':
Found '_printf', possibly from 'printf' (C)
Object: 'matrix.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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pair.compare 5.407 0.228 5.684
* 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/GlobalAncova.Rcheck/00check.log'
for details.
* installing *source* package 'GlobalAncova' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c GlobalAncova.c -o GlobalAncova.o
GlobalAncova.c:31:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tDD = (double *) malloc ( (*sD)*(*sD)*sizeof(double) ) ;
˜˜˜˜˜^˜˜˜˜˜˜
GlobalAncova.c:34:12: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*sD)*(*sD)*sizeof(double));
˜˜˜˜˜^˜˜˜˜˜˜
GlobalAncova.c:36:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tmp = (double *) malloc ( (*sD)*(*sD)*sizeof(double) ) ;
˜˜˜˜˜^˜˜˜˜˜˜
GlobalAncova.c:39:12: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*sD)*(*sD)*sizeof(double) );
˜˜˜˜˜^˜˜˜˜˜˜
GlobalAncova.c:41:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tmp2 = (double *) malloc ( (*zD)*(*sD)*sizeof(double) ) ;
˜˜˜˜˜^˜˜˜˜˜˜
GlobalAncova.c:44:12: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*zD)*(*sD)*sizeof(double) );
˜˜˜˜˜^˜˜˜˜˜˜
GlobalAncova.c:46:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tmp3 = (double *) malloc ( (*zD)*(*zD)*sizeof(double) ) ;
˜˜˜˜˜^˜˜˜˜˜˜
GlobalAncova.c:49:12: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*zD)*(*zD)*sizeof(double) );
˜˜˜˜˜^˜˜˜˜˜˜
GlobalAncova.c:86:40: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
R_full = (double *) malloc ( (*zxx)*(*zD_full) * sizeof(double) );
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:89:13: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*zxx)*(*zD_full) * sizeof(double) );
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:98:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
R_red = (double *) malloc ( (*zxx)*(*zD_red) * sizeof(double) );
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:101:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*zxx)*(*zD_red) * sizeof(double) );
˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:146:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
SS_full_i = (double *) malloc ( (*zrr) * sizeof(double)) ;
^˜˜˜ ˜
GlobalAncova.c:149:7: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*zrr) * sizeof(double) );
^˜˜˜ ˜
GlobalAncova.c:151:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
SS_extra_i = (double *) malloc ( (*zrr) * sizeof(double)) ;
^˜˜˜ ˜
GlobalAncova.c:154:6: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*zrr) * sizeof(double));
^˜˜˜ ˜
GlobalAncova.c:156:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
F_perm = (double *) malloc ( (*n_test_genes) * sizeof(double));
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:159:6: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*n_test_genes) * sizeof(double));
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:161:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tDD_perm = (double *) malloc ( (*sD_full)*(*sD_full) * sizeof(double)) ;
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:164:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*sD_full)*(*sD_full) * sizeof(double));
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:168:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ord_perm = (int *) malloc ( (*N_Subjects) * sizeof(int) ) ;
^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:171:8: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*N_Subjects) * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:248:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
SS_full_i = (double *) malloc ( (*zrr) * sizeof(double)) ;
^˜˜˜ ˜
GlobalAncova.c:251:7: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*zrr) * sizeof(double) );
^˜˜˜ ˜
GlobalAncova.c:253:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
SS_extra_i = (double *) malloc ( (*zrr) * sizeof(double)) ;
^˜˜˜ ˜
GlobalAncova.c:256:6: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*zrr) * sizeof(double));
^˜˜˜ ˜
GlobalAncova.c:258:37: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
F_perm = (double *) malloc ( (*n_test_genes) * sizeof(double));
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:261:6: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*n_test_genes) * sizeof(double));
^˜˜˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:263:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
tDD_perm = (double *) malloc ( (*sD_full)*(*sD_full) * sizeof(double)) ;
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:266:15: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*sD_full)*(*sD_full) * sizeof(double));
˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:270:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
ord_perm = (int *) malloc ( (*N_Subjects) * sizeof(int) ) ;
^˜˜˜˜˜˜˜˜˜˜ ˜
GlobalAncova.c:273:8: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
(*N_Subjects) * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
32 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ludcmp.c -o ludcmp.o
ludcmp.c:37:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
vv = (double *) malloc(n * sizeof(double));
^ ˜
ludcmp.c:189:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if ( ( col = (double *) malloc((*n) * sizeof(double)) ) == NULL )
^˜ ˜
ludcmp.c:192:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if ( ( indx = (int *) malloc((*n) * sizeof(int)) ) == NULL )
^˜ ˜
ludcmp.c:223:33: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if ( ( indx = (int *) malloc((*n) * sizeof(int)) ) == NULL )
^˜ ˜
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 matrix.c -o matrix.o
matrix.c:32:10: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
srand ( (int) (seed) ) ;
˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
1 warning 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 GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GlobalAncova.Rcheck/GlobalAncova/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 (GlobalAncova)