SAGx 1.18.0
Per Broberg,
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/SAGx | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | 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 (10.5.8) / i386 | OK | [ OK ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/SAGx.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SAGx/DESCRIPTION' ... OK
* this is package 'SAGx' version '1.18.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SAGx' 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 whether the name space 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 ... NOTE
Fstat: no visible binding for global variable ‘M’
GSEA.mean.t: no visible binding for global variable ‘samroc.res’
GSEA.mean.t: no visible binding for global variable ‘kegg’
GSEA.mean.t : maxmeanf: no visible binding for global variable
‘plustat’
R2BASE: no visible binding for global variable ‘clingen’
R2BASE: no visible binding for global variable ‘AZID’
R2BASE: no visible binding for global variable ‘dats’
R2BASE: no visible binding for global variable ‘annots’
R2mim: no visible binding for global variable ‘inm’
Xprep: no visible binding for global variable ‘M’
Xprep.resid: no visible binding for global variable ‘M’
clin2mim: no visible binding for global variable ‘dbs’
clin2mim: no visible binding for global variable ‘clinical’
estimatep0: no visible binding for global variable ‘pp’
fetchSignal: no visible global function definition for ‘sqlQuery’
fp.fn: no visible binding for global variable ‘pvals’
gap: no visible binding for global variable ‘g’
list.experiments: no visible global function definition for ‘sqlQuery’
mat2TeX: no visible global function definition for ‘errif’
p0.mom: no visible binding for global variable ‘pvalues’
pava.fdr: no visible binding for global variable ‘pvalues’
rank.genes: no visible binding for global variable ‘indats’
rank.trend: no visible binding for global variable ‘x’
rsd.test: no visible binding for global variable ‘x’
rsd.test: no visible binding for global variable ‘y’
samrocN: no visible binding for global variable ‘M’
samrocNboot: no visible binding for global variable ‘M’
* checking Rd files ... OK
* checking Rd files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package ‘SAGx’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c minigsea.c -o minigsea.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c newboot.c -o newboot.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -c samrocNboot.c -o samrocNboot.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 SAGx.so minigsea.o newboot.o samrocNboot.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c minigsea.c -o minigsea.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c newboot.c -o newboot.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c samrocNboot.c -o samrocNboot.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o SAGx.so minigsea.o newboot.o samrocNboot.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c minigsea.c -o minigsea.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c newboot.c -o newboot.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c samrocNboot.c -o samrocNboot.o
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o SAGx.so minigsea.o newboot.o samrocNboot.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c minigsea.c -o minigsea.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c newboot.c -o newboot.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -c samrocNboot.c -o samrocNboot.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o SAGx.so minigsea.o newboot.o samrocNboot.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
*** installing help indices
>>> Building/Updating help pages for package 'SAGx'
Formats: text html latex example
Fstat text html latex example
GSEA.mean.t text html latex
JT.test text html latex example
R2BASE text html latex
R2mim text html latex
Xprep text html latex
Xprep.resid text html latex
clin2mim text html latex
cluster.q text html latex
estimatep0 text html latex
fetchSignal text html latex example
firstpass text html latex example
fom text html latex
fp.fn text html latex
gap text html latex example
list.experiments text html latex example
list.intersection.p text html latex
mat2TeX text html latex
myclus text html latex example
normalise text html latex
one.probeset.per.gene text html latex
outlier text html latex example
p0.mom text html latex
pava.fdr text html latex
pava text html latex example
rank.genes text html latex
rank.trend text html latex example
rsd.test text html latex
samroc.result-class text html latex
samrocn text html latex
samrocnboot text html latex example
union.of.pways text html latex example
** building package indices ...
* DONE (SAGx)