plier 1.12.0
Crispin Miller
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/plier | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | [ OK ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/plier.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'plier/DESCRIPTION' ... OK
* this is package 'plier' version '1.12.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'plier' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 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 cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating plier-Ex.R ... OK
* checking examples ... OK
* creating plier-manual.tex ... OK
* checking plier-manual.tex using pdflatex ... OK
* Installing *source* package 'plier' ...
** libs
** arch - i386
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c affyplier.cpp -o affyplier.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c plier_impl.cpp -o plier_impl.o
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:910: warning: 'LogLikelihood' may be used uninitialized in this function
plieralg.cpp: At global scope:
plieralg.cpp:49: warning: 'g_ErrorCode' defined but not used
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c rwrapper.cpp -o rwrapper.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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
** arch - ppc
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c affyplier.cpp -o affyplier.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c plier_impl.cpp -o plier_impl.o
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:910: warning: 'LogLikelihood' may be used uninitialized in this function
plieralg.cpp: At global scope:
plieralg.cpp:49: warning: 'g_ErrorCode' defined but not used
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c rwrapper.cpp -o rwrapper.o
g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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
** arch - ppc64
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c affyplier.cpp -o affyplier.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c plier_impl.cpp -o plier_impl.o
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:910: warning: 'LogLikelihood' may be used uninitialized in this function
plieralg.cpp: At global scope:
plieralg.cpp:49: warning: 'g_ErrorCode' defined but not used
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c rwrapper.cpp -o rwrapper.o
g++-4.2 -arch ppc64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c affyplier.cpp -o affyplier.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c plier_impl.cpp -o plier_impl.o
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c plieralg.cpp -o plieralg.o
plieralg.cpp: In function 'long int NewtonPlier(plier_data*, double&)':
plieralg.cpp:910: warning: 'LogLikelihood' may be used uninitialized in this function
plieralg.cpp: At global scope:
plieralg.cpp:49: warning: 'g_ErrorCode' defined but not used
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c rwrapper.cpp -o rwrapper.o
g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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
** R
** preparing package for lazy loading
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
>>> Building/Updating help pages for package 'plier'
Formats: text html latex example
Note: removing empty section \examples in file 'justPlier.Rd'
justPlier text html latex
** building package indices ...
* DONE (plier)