metahdep 1.18.0 John R. Stevens
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/metahdep | 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/metahdep.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 'metahdep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metahdep' version '1.18.0'
* 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 'metahdep' 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: metahdep.other.Rd:40-42: Dropping empty section \usage
prepare_Rd: metahdep.other.Rd:43-45: Dropping empty section \arguments
prepare_Rd: metahdep.other.Rd:46-48: Dropping empty section \value
* 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 ... [7s/7s] 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 was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/metahdep.Rcheck/00check.log'
for details.
* installing *source* package 'metahdep' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c metahdep.c -o metahdep.o
metahdep.c:71:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
temp_array = (int *) R_alloc((last - first + 1), sizeof(int));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
metahdep.c:107:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
sort_index = (int *) R_alloc(num_names, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
metahdep.c:155:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
index_ptr_array = (int**) R_alloc(num_studies, sizeof(int *));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
metahdep.c:163:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
index_ptr_array[i] = (int *) R_alloc(study_length, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
metahdep.c:174:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
list_elements = (SEXP *) R_alloc(num_studies, sizeof(SEXP));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
metahdep.c:451:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
study = (int *) R_alloc(max_rows, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
metahdep.c:452:24: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
row = (int *) R_alloc(max_rows, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
metahdep.c:471:79: warning: incompatible pointer to integer conversion passing 'const char *' to parameter of type 'char' [-Wint-conversion]
index = metan_binary_search_unique(name_list, sort_index, R_old_names, j, CHAR(STRING_ELT(R_old_chipsets, j)), i);
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:395:18: note: expanded from macro 'CHAR'
#define CHAR(x) R_CHAR(x)
^˜˜˜˜˜˜˜˜
metahdep.c:372:103: note: passing argument to parameter 'chipset_name' here
SEXP metan_binary_search_unique(SEXP name_list, SEXP sort_index, SEXP gene_name, int gene_index, char chipset_name, int study_num)
^
metahdep.c:483:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
study = (int *) R_alloc(max_rows, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
metahdep.c:484:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
row = (int *) R_alloc(max_rows, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
10 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 metahdep.so metahdep.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/metahdep.Rcheck/metahdep/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 (metahdep)