BioC 2.13: CHECK report for pcaGoPromoter on moscato1

Package: pcaGoPromoter

Version: 1.6.0

Command: rm -rf pcaGoPromoter.buildbin-libdir && mkdir pcaGoPromoter.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pcaGoPromoter.buildbin-libdir pcaGoPromoter_1.6.0.tar.gz >pcaGoPromoter-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=pcaGoPromoter.buildbin-libdir --install="check:pcaGoPromoter-install.out" --force-multiarch --no-vignettes --timings pcaGoPromoter_1.6.0.tar.gz && mv pcaGoPromoter.buildbin-libdir/* pcaGoPromoter.Rcheck/ && rmdir pcaGoPromoter.buildbin-libdir

StartedAt: 2014-04-05 05:43:55 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:51:37 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 461.4 seconds

RetCode: 0

Status:  OK

CheckDir: pcaGoPromoter.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/pcaGoPromoter.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pcaGoPromoter/DESCRIPTION' ... OK
* this is package 'pcaGoPromoter' version '1.6.0'
* 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 whether package 'pcaGoPromoter' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'ellipse' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'Biobase'
  All declared Imports should be used.
Package in Depends field not imported from: 'ellipse'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
primoData.getPromoters: no visible global function definition for
  'readFASTA'
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'pcaGoPromoter.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [177s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GOtree 95.32   2.06  105.84
primo  58.49   0.49   63.44
** running examples for arch 'x64' ... [167s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GOtree 98.47   1.70  100.17
primo  57.64   0.51   58.16
pca     4.73   0.02    5.59
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/pcaGoPromoter.Rcheck/00check.log'
for details.

install for i386

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

install for x64

* installing *source* package 'pcaGoPromoter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaGoPromoter' as pcaGoPromoter_1.6.0.zip
* DONE (pcaGoPromoter)

name	user	system	elapsed
GOtree	95.32	2.06	105.84
pca	3.62	0.06	3.68
pcaGoPromoter-package	0	0	0
primo	58.49	0.49	63.44
primoData	0	0	0

name	user	system	elapsed
GOtree	98.47	1.70	100.17
pca	4.73	0.02	5.59
pcaGoPromoter-package	0	0	0
primo	57.64	0.51	58.16
primoData	0	0	0