plier 1.30.0
Crispin Miller
| 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/plier | | 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 | WARNINGS | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/plier.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 'plier/DESCRIPTION' ... OK
* this is package 'plier' version '1.30.0'
* 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 'plier' can be installed ... [5s/5s] 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: justPlier.Rd:50-52: Dropping empty section \examples
* 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 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 ... WARNING
File '/Users/biocbuild/bbs-2.12-bioc/meat/plier.Rcheck/plier/libs/plier.so':
Found '___stderrp', possibly from 'stderr' (C)
Object: 'rwrapper.o'
Found '_exit', possibly from 'exit' (C)
Object: 'rwrapper.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 examples ... NONE
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/plier.Rcheck/00check.log'
for details.
* installing *source* package 'plier' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c affyplier.cpp -o affyplier.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c plier_impl.cpp -o plier_impl.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c plieralg.cpp -o plieralg.o
plieralg.cpp:491:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonCDeriv, 0, pData->m_nAnalyses*sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
plieralg.cpp:492:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonCGrad, 0, pData->m_nAnalyses*sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
plieralg.cpp:493:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonADeriv, 0, pData->m_nProbes*sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
plieralg.cpp:494:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonAGrad, 0, pData->m_nProbes*sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
plieralg.cpp:1164:35: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonAStep, 0, pData->m_nProbes*sizeof(double)); // no change to affinities based on data
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
plieralg.cpp:49:12: warning: unused variable 'g_ErrorCode' [-Wunused-variable]
static int g_ErrorCode=NoError;
^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp:75:31: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sp->set_sea_attenuation(attenuation);
˜˜ ^˜˜˜˜˜˜˜˜˜˜
rwrapper.cpp:79:30: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sp->set_plier_gmcutoff(gmcutoff);
˜˜ ^˜˜˜˜˜˜˜
rwrapper.cpp:80:34: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sp->set_plier_probepenalty(probepenalty);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
rwrapper.cpp:81:33: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sp->set_plier_concpenalty(concpenalty);
˜˜ ^˜˜˜˜˜˜˜˜˜˜
rwrapper.cpp:263:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pms = (double *) R_alloc(MAX_PROBESET_SIZE * *num_exp,sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
rwrapper.cpp:268:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mms = (double *) R_alloc(MAX_PROBESET_SIZE * *num_exp,sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
rwrapper.cpp:275:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pm_ptr = (double **) R_alloc(*num_exp,sizeof(double *));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
rwrapper.cpp:280:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mm_ptr = (double **) R_alloc(*num_exp,sizeof(double *));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
8 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 plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/plier.Rcheck/plier/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (plier)