BioC 2.10: CHECK report for edgeR on moscato2

Package: edgeR

Version: 2.6.12

Command: rm -rf edgeR.buildbin-libdir && mkdir edgeR.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=edgeR.buildbin-libdir edgeR_2.6.12.tar.gz >edgeR-install.out 2>&1 && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD check --library=edgeR.buildbin-libdir --install="check:edgeR-install.out" --force-multiarch --no-vignettes --timings edgeR_2.6.12.tar.gz && mv edgeR.buildbin-libdir/* edgeR.Rcheck/ && rmdir edgeR.buildbin-libdir

StartedAt: 2012-09-24 00:29:16 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:31:19 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 122.6 seconds

RetCode: 0

Status: OK

CheckDir: edgeR.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.10-bioc/meat/edgeR.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'edgeR/DESCRIPTION' ... OK
* this is package 'edgeR' version '2.6.12'
* 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 whether package 'edgeR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
mglmLevenberg: warning in glmnb.fit(X = X, y = z, dispersion =
  dispersion[i], offset = offset[i, ], start = start[i, ]): partial
  argument match of 'start' to 'start.method'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'edgeR-Tests.R'
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ...416c416
< [1] 0.53374778 0.20168294 4.18933146 0.69542655 0.00796757
---
> [1] 0.53374778 0.20168294 4.18933184 0.69542655 0.00796757
442,446c442,446
< Gene1 3.128148 16.522832 99.713625
< Gene2 4.522517  5.858801  8.671818
< Gene3 1.169726  2.402414  5.637468
< Gene4 4.176370  4.709091  6.066636
< Gene5 2.072116  3.834708  8.108178
---
> Gene1 3.128147 16.522846 99.713802
> Gene2 4.522480  5.858800  8.671883
> Gene3 1.169671  2.402414  5.637736
> Gene4 4.176397  4.709091  6.066597
> Gene5 2.072114  3.834707  8.108180
 OK
** running tests for arch 'x64'
  Running 'edgeR-Tests.R'
  Comparing 'edgeR-Tests.Rout' to 'edgeR-Tests.Rout.save' ...416c416
< [1] 0.53374778 0.20168294 4.18933146 0.69542655 0.00796757
---
> [1] 0.53374778 0.20168294 4.18933184 0.69542655 0.00796757
442,446c442,446
< Gene1 3.128148 16.522832 99.713625
< Gene2 4.522517  5.858801  8.671818
< Gene3 1.169726  2.402414  5.637468
< Gene4 4.176370  4.709091  6.066636
< Gene5 2.072116  3.834708  8.108178
---
> Gene1 3.128147 16.522846 99.713802
> Gene2 4.522480  5.858800  8.671883
> Gene3 1.169671  2.402414  5.637736
> Gene4 4.176397  4.709091  6.066597
> Gene5 2.072114  3.834707  8.108180
 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
  'E:/biocbld/bbs-2.10-bioc/meat/edgeR.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'edgeR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'edgeR.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'edgeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'edgeR' as edgeR_2.6.12.zip

* DONE (edgeR)

Summary

Command output