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Package 79/251HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: gcrma
Version: 2.11.1
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check gcrma_2.11.1.tar.gz
StartedAt: 2007-12-11 06:02:56 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 06:09:57 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 421.6 seconds
RetCode: 0
Status: WARNINGS
CheckDir: gcrma.Rcheck
Warnings: 1

Command output

* 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

gcrma.Rcheck/00install.out:

/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)