gcrma 2.11.1
Z. Wu
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gcrma | | Last Changed Rev: 28347 / Revision: 29143 | | Last Changed Date: 2007-10-31 09:11:12 -0700 (Wed, 31 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | WARNINGS | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | WARNINGS | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | [ WARNINGS ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | WARNINGS | OK |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/gcrma.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'gcrma/DESCRIPTION' ... OK
* this is package 'gcrma' version '2.11.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'gcrma' 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
compute.affinities: no visible binding for global variable
‘affinity.spline.coefs’
compute.affinities2: no visible binding for global variable
‘affinity.spline.coefs’
compute.affinities.nomm: no visible binding for global variable
‘affinity.spline.coefs’
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'bg.adjust.affinities':
bg.adjust.affinities
Code: function(pms, ncs, apm, anc, index.affinities, k = k, fast =
FALSE, nomm = FALSE)
Docs: function(pms, ncs, apm, anc, index.affinities, k = k, fast)
Argument names in code not in docs:
nomm
Mismatches in argument default values:
Name: fast Code: FALSE Docs:
Codoc mismatches from documentation object 'bg.parameters.ns':
bg.parameters.ns
Code: function(x, affinities, affinities2 = NULL, affinities3 = NULL,
span = 0.2)
Docs: function(x, affinities, affinities2, affinities3)
Argument names in code not in docs:
span
Mismatches in argument default values:
Name: affinities2 Code: NULL Docs:
Name: affinities3 Code: NULL Docs:
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... 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 gcrma-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './gcrma2.0.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './gcrma2.0.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './gcrma2.0.tex' ...
* creating gcrma-manual.tex ... OK
* checking gcrma-manual.tex ... OK
WARNING: There was 1 warning, see
/loc/home/biocbuild/bbs-2.2-bioc/meat/gcrma.Rcheck/00check.log
for details
/loc/home/biocbuild/bbs-2.2-bioc/meat/gcrma.Rcheck
* Installing *source* package 'gcrma' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c computeAffinities.c -o computeAffinities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c postmean.c -o postmean.o
gcc -std=gnu99 -shared -L/usr/local/lib -o gcrma.so baseProfile.o computeAffinities.o postmean.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
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)'.
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: matchprobes
Loading required package: splines
** help
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
>>> Building/Updating help pages for package 'gcrma'
Formats: text html latex example
affinity.spline.coefs text html latex
bg.adjust.affinities text html latex
bg.adjust.gcrma text html latex example
bg.parameters.ns text html latex
compute.affinities text html latex
fast.bkg text html latex
gcrma text html latex example
gcrma.engine text html latex
gcrma.engine2 text html latex
getCDF text html latex
justGCRMA text html latex
** building package indices ...
* DONE (gcrma)