BicARE 1.18.0
Pierre Gestraud
| 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/BicARE | | 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/BicARE.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 'BicARE/DESCRIPTION' ... OK
* this is package 'BicARE' 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 'BicARE' can be installed ... [19s/19s] 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 ... 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/BicARE.Rcheck/BicARE/libs/BicARE.so':
Found '_printf', possibly from 'printf' (C)
Object: 'BicARE.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 ... [16m/16m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
testSet 689.127 4.015 708.811
FLOC 251.569 0.915 257.491
makeReport 6.085 0.188 6.637
* 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/BicARE.Rcheck/00check.log'
for details.
* installing *source* package 'BicARE' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BicARE.c -o BicARE.o
BicARE.c:126:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
nrowBic = vecResvolBic[z * 4 + 2];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:127:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
ncolBic = vecResvolBic[z * 4 + 3];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:280:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
nrowBic = vecResvolBic[z * 4 + 2];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:281:16: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
ncolBic = vecResvolBic[z * 4 + 3];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:282:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
volBic = vecResvolBic[z * 4 + 1];
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:426:35: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *bicRow2 =(int *) R_alloc((long)(*k * *nrowData), sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:427:36: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *bicCol2 = (int *) R_alloc((long)(*k * *ncolData), sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:428:37: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *vecOrder = (int *) R_alloc((long)(total), sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:429:46: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *vecBestGain = (double *) R_alloc((long)(total), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:430:39: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
int *vecBestBic = (int *) R_alloc((long)(total), sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:431:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *sumRow = (double *) R_alloc((long)(*k * *nrowData), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:432:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *sumCol = (double *) R_alloc((long)(*k * *ncolData), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:433:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *sumBic = (double *) R_alloc((long)(*k), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
BicARE.c:434:42: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *sumRow2 = (double *) R_alloc((long)(*k * *nrowData), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:435:42: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *sumCol2 = (double *) R_alloc((long)(*k * *ncolData), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:436:42: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *sumBic2 = (double *) R_alloc((long)(*k), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
BicARE.c:441:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bicRow2, bicRow, *k * *nrowData * sizeof(int));
˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
BicARE.c:441:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bicRow2, bicRow, *k * *nrowData * sizeof(int));
˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
BicARE.c:442:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bicCol2, bicCol, *k * *ncolData * sizeof(int));
˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
BicARE.c:442:32: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(bicCol2, bicCol, *k * *ncolData * sizeof(int));
˜˜˜^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
BicARE.c:439:12: warning: unused variable 'invk' [-Wunused-variable]
double invk = 1/(double)*k;
^
BicARE.c:501:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *sumRow = (double *) R_alloc((long)(*nrowData), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BicARE.c:502:41: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double *sumCol = (double *) R_alloc((long)(*ncolData), sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
23 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 BicARE.so BicARE.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BicARE.Rcheck/BicARE/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 (BicARE)