genefilter 1.42.0
Bioconductor Package Maintainer
| 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/genefilter | | 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 | WARNINGS | |
| 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/genefilter.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 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.42.0'
* 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 'genefilter' can be installed ... [17s/18s] 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
eSetFilter : buildGUI: no visible binding for '<<-' assignment to 'END'
eSetFilter : buildGUI : finish: no visible binding for '<<-' assignment
to 'END'
eSetFilter : buildGUI: no visible binding for global variable 'END'
* 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 ... [34s/37s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
rowFtests 12.018 0.377 13.348
half.range.mode 9.172 0.118 9.943
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'RColorBrewer'
* 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/genefilter.Rcheck/00check.log'
for details.
* installing *source* package 'genefilter' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c half_range_mode.cpp -o half_range_mode.o
half_range_mode.cpp:54:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for ( i = 0; i < (int) counts.size(); i++ ) if ( counts[i] == N_prime ) J.push_back( i );
˜˜˜˜˜˜ ^
half_range_mode.cpp:67:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for ( i = 0; i < (int) J.size(); i++ ) w_range.push_back( start[ J[i] + N_prime - 1 ] - start[ J[i] ] );
˜ ^
half_range_mode.cpp:67:104: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for ( i = 0; i < (int) J.size(); i++ ) w_range.push_back( start[ J[i] + N_prime - 1 ] - start[ J[i] ] );
˜ ^
half_range_mode.cpp:73:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
while( w_range[ i ] > w_prime ) i++;
˜˜˜˜˜˜˜ ^
half_range_mode.cpp:74:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
new_start = start + J[i];
˜ ^
half_range_mode.cpp:75:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
new_end = start + J[i] + N_prime;
˜ ^
half_range_mode.cpp:79:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for ( i++; i < (int) J.size(); i++ ) if ( w_range[ i ] == w_prime ) new_end = start + J[i] + N_prime;
˜˜˜˜˜˜˜ ^
half_range_mode.cpp:79:95: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for ( i++; i < (int) J.size(); i++ ) if ( w_range[ i ] == w_prime ) new_end = start + J[i] + N_prime;
˜ ^
half_range_mode.cpp:21:11: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
N = end - start;
˜ ˜˜˜˜^˜˜˜˜˜˜
half_range_mode.cpp:89:30: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
N_double_prime = new_end - new_start;
˜ ˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜
10 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c nd.c -o nd.o
nd.c:242:12: warning: unused variable 'w1' [-Wunused-variable]
double w1, w2; /* Weighted values */
^
nd.c:242:16: warning: unused variable 'w2' [-Wunused-variable]
double w1, w2; /* Weighted values */
^
nd.c:300:29: warning: implicit conversion changes signedness: 'RSInt' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
tmp = (gene_t *)R_alloc(*nr, sizeof(gene_t));
˜˜˜˜˜˜˜ ^˜˜
nd.c:336:13: warning: implicit conversion changes signedness: 'RSInt' (aka 'int') to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(tmp, *nr, sizeof(gene_t), distCompare);
˜˜˜˜˜ ^˜˜
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 pAUC.c -o pAUC.o
pAUC.c:24:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
x = (double *) R_alloc(columns+1, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
pAUC.c:25:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
y = (double *) R_alloc(columns+1, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜^˜
pAUC.c:123:9: warning: unused variable 'i' [-Wunused-variable]
int i;
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rowPAUCs.c -o rowPAUCs.o
rowPAUCs.c:25:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
x = (double *) R_alloc(ncc+1, sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜^˜
rowPAUCs.c:26:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
y = (double *) R_alloc(ncc+1, 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 rowttests.c -o rowttests.o
rowttests.c:41:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
s[grp] = (double*) R_alloc(nt, sizeof(double));
˜˜˜˜˜˜˜ ^˜
rowttests.c:42:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ss[grp] = (double*) R_alloc(nt, sizeof(double));
˜˜˜˜˜˜˜ ^˜
2 warnings generated.
gfortran-4.2 -arch x86_64 -fPIC -g -O2 -Wall -pedantic -c ttest.f -o ttest.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/genefilter.Rcheck/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'genefilter'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefilter)