BioC 2.12: CHECK report for cellHTS2 on moscato2

Package: cellHTS2

Version: 2.24.1

Command: rm -rf cellHTS2.buildbin-libdir && mkdir cellHTS2.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.24.1.tar.gz >cellHTS2-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.24.1.tar.gz && mv cellHTS2.buildbin-libdir/* cellHTS2.Rcheck/ && rmdir cellHTS2.buildbin-libdir

StartedAt: 2013-10-09 01:24:02 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:33:58 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 595.8 seconds

RetCode: 0

Status:  OK

CheckDir: cellHTS2.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/cellHTS2.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellHTS2/DESCRIPTION' ... OK
* this is package 'cellHTS2' version '2.24.1'
* 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 'cellHTS2' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      1.7Mb
* 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
* 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
annotate,cellHTS: warning in read.table(file.path(path, file), sep =
  "\t", header = TRUE, stringsAsFactors = FALSE, na.string = "", quote
  = "", fill = FALSE): partial argument match of 'na.string' to
  'na.strings'
* 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' ... [57s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
Bscore 5.89      0     5.9
** running examples for arch 'x64' ... [62s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
Bscore 7.07   0.01    7.09
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'test.R' [69s]
 [70s] OK
** running tests for arch 'x64'
  Running 'test.R' [77s]
 [77s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'GO.db' 'KEGG.db'
* 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 were 3 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/cellHTS2.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'cellHTS2' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'lines' from package 'graphics' in package 'cellHTS2'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'cellHTS2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellHTS2' as cellHTS2_2.24.1.zip
* DONE (cellHTS2)