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BioC 2.12: CHECK report for copa on george2

This page was generated on 2013-10-09 09:37:19 -0700 (Wed, 09 Oct 2013).

Package 149/671HostnameOS / ArchBUILDCHECKBUILD BIN
copa 1.28.0
James W. MacDonald
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/copa
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: copa
Version: 1.28.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings copa_1.28.0.tar.gz
StartedAt: 2013-10-09 01:09:02 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:09:48 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 45.6 seconds
RetCode: 0
Status:  OK 
CheckDir: copa.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/copa.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copa/DESCRIPTION’ ... OK
* this is package ‘copa’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘copa’ can be installed ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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
copa: warning in matrix(1:dim(mat)[1], nc = dim(mat)[1], nr =
  dim(mat)[1]): partial argument match of 'nr' to 'nrow'
copa: warning in matrix(1:dim(mat)[1], nc = dim(mat)[1], nr =
  dim(mat)[1]): partial argument match of 'nc' to 'ncol'
pSum: warning in matrix(out, nc = length(a), nr = length(a)): partial
  argument match of 'nr' to 'nrow'
pSum: warning in matrix(out, nc = length(a), nr = length(a)): partial
  argument match of 'nc' to 'ncol'
plotCopa: warning in matrix(1:2, nc = 1): partial argument match of
  'nc' to 'ncol'
pSum: no visible binding for global variable ‘mat’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/copa.Rcheck/00check.log’
for details.

copa.Rcheck/00install.out:

* installing *source* package ‘copa’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -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-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/copa.Rcheck/copa/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (copa)

copa.Rcheck/copa-Ex.timings:

nameusersystemelapsed
copa0.2520.0040.253
copaTable0.2160.0040.221
plotCopa0.0120.0000.014
scatterPlotCopa0.0120.0000.013
summaryCopa0.0040.0080.014