puma 2.5.0
Richard Pearson , Li Zhang
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/puma | | Last Changed Rev: 54810 / Revision: 55359 | | Last Changed Date: 2011-04-13 18:14:51 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/puma.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘puma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘puma’ version ‘2.5.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘puma’ can be installed ... OK
* checking installed package size ... 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 whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... WARNING
S4 class codoc mismatches from documentation object 'exprReslt-class':
Slots for class 'exprReslt'
Code: .__classVersion__ annotation assayData experimentData
featureData phenoData prcfifty prcfive prcninfive prcsevfive
prctwfive protocolData
Inherited: experimentData assayData phenoData featureData annotation
protocolData .__classVersion__
Docs: annotation description exprs notes phenoData prcfifty prcfive
prcninfive prcsevfive prctwfive se.exprs
* 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 sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘puma.pdf’ from 268Kb to 145Kb
consider running tools::compactPDF() on these files
* checking examples ... OK
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
‘/Users/biocbuild/bbs-2.9-bioc/meat/puma.Rcheck/00check.log’
for details
* installing *source* package ‘puma’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c cregistration.c -o cregistration.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c donlp2.c -o donlp2.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c ipplr_c.c -o ipplr_c.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c multimgmos.c -o multimgmos.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c newx.c -o newx.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c pplr_c.c -o pplr_c.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c pumaclust_c.c -o pumaclust_c.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c pumaclustii_c.c -o pumaclustii_c.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c user_eval.c -o user_eval.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o puma.so cregistration.o donlp2.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld warning: codegen in _user_eval (offset 0x0000028F) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x00000305) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x00000397) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x0000040F) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x0000049A) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x0000050F) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x000007E2) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x00000805) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x0000096A) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x000009F0) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x00000C69) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x00000D9E) prevents image from loading in dyld shared cache
ld warning: codegen in _user_eval (offset 0x00000DAF) prevents image from loading in dyld shared cache
installing to /Users/biocbuild/bbs-2.9-bioc/meat/puma.Rcheck/puma/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
by using mclust, invoked on its own or through another package,
you accept the license agreement in the mclust LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
by using mclust, invoked on its own or through another package,
you accept the license agreement in the mclust LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt
* DONE (puma)