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Package 54/251HostnameOS / ArchBUILDCHECKBUILD BIN
copa 1.7.0
James W. MacDonald
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/copa
Last Changed Rev: 28083 / Revision: 29143
Last Changed Date: 2007-10-19 13:14:15 -0700 (Fri, 19 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  OK  OK 
Package: copa
Version: 1.7.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check copa_1.7.0.tar.gz
StartedAt: 2007-12-11 05:44:12 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 05:45:39 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 86.8 seconds
RetCode: 0
Status: OK
CheckDir: copa.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/copa.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'copa/DESCRIPTION' ... OK
* this is package 'copa' version '1.7.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'copa' 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
pSum: no visible binding for global variable ‘mat’
* checking Rd files ... 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
* creating copa-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' './copa.tex' ...
Package natbib Warning: Citation `Rowley:2001' on page 1 undefined on input lin
Package natbib Warning: Citation `Tomlins:2005' on page 1 undefined on input li
Package natbib Warning: Citation `Fonseca:2004' on page 1 undefined on input li
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './copa.tex' ...
Package natbib Warning: Citation `Rowley:2001' on page 1 undefined on input lin
Package natbib Warning: Citation `Tomlins:2005' on page 1 undefined on input li
Package natbib Warning: Citation `Fonseca:2004' on page 1 undefined on input li
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './copa.tex' ...
* creating copa-manual.tex ... OK
* checking copa-manual.tex ... OK

copa.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/copa.Rcheck
* Installing *source* package 'copa' ...
** 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 copa.c -o copa.o
gcc -std=gnu99 -shared -L/usr/local/lib -o copa.so copa.o   -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** 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)'.

** help
 >>> Building/Updating help pages for package 'copa'
     Formats: text html latex example 
  copa                              text    html    latex   example
  copa.package                      text    html    latex
  copaFilter                        text    html    latex
  copaPerm                          text    html    latex
  copaTable                         text    html    latex   example
  getans                            text    html    latex
  pSum                              text    html    latex
  perm.mat                          text    html    latex
  plotCopa                          text    html    latex   example
  scatterPlotCopa                   text    html    latex   example
  summaryCopa                       text    html    latex   example
** building package indices ...
* DONE (copa)