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Package 171/251HostnameOS / ArchBUILDCHECKBUILD BIN
pickgene 1.11.0
Brian S. Yandell
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pickgene
Last Changed Rev: 27716 / Revision: 29143
Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 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: pickgene
Version: 1.11.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check pickgene_1.11.0.tar.gz
StartedAt: 2007-12-11 07:47:11 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 07:48:11 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 59.3 seconds
RetCode: 0
Status: WARNINGS
CheckDir: pickgene.Rcheck
Warnings: 1

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/pickgene.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'pickgene/DESCRIPTION' ... OK
* this is package 'pickgene' version '1.11.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'pickgene' 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 ... NOTE
lod.plot: possible error in oddsplot(exp(data[[x]]), exp(data[[y]]),
  theta, col = col, xlab = xlab, ylab = ylab, chip = ""): unused
  argument(s) (chip = "")
nloglik: no visible binding for global variable ‘.fit.xx’
nloglik: no visible binding for global variable ‘.fit.yy’
nploglik: no visible binding for global variable ‘.fit.xx’
nploglik: no visible binding for global variable ‘.fit.yy’
nploglik: no visible binding for global variable ‘.fit.zz’
s.check1: no visible global function definition for ‘lod’
shrinkplot: no visible global function definition for ‘s.fits’
shrinkplot: no visible binding for global variable ‘lims’
s.marg: no visible binding for global variable ‘x’
* checking Rd files ... WARNING
Rd files without 'description':
  Simulation.pickgene.Rd
These entries are required in an Rd file.

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating pickgene-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' './pickgene.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './pickgene.tex' ...
* creating pickgene-manual.tex ... OK
* checking pickgene-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/home/biocbuild/bbs-2.2-bioc/meat/pickgene.Rcheck/00check.log
for details

pickgene.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/pickgene.Rcheck
* Installing *source* package 'pickgene' ...
** R
** inst
** preparing package for lazy loading
Loading required package: MASS
** help
Note: ignoring empty \keyword entries
Note: removing empty section \usage
Note: removing empty section \details
Note: removing empty section \description
 >>> Building/Updating help pages for package 'pickgene'
     Formats: text html latex example 
  Simulation.pickgene               text    html    latex   example
  em.ggb                            text    html    latex   example
  model.pickgene                    text    html    latex   example
  oddsplot                          text    html    latex   example
  pickgene-internal                 text    html    latex
  pickgene                          text    html    latex   example
  robustscale                       text    html    latex   example
** building package indices ...
* DONE (pickgene)