BioC 2.13: CHECK report for MiRaGE on moscato1

Package: MiRaGE

Version: 1.4.0

Command: rm -rf MiRaGE.buildbin-libdir && mkdir MiRaGE.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MiRaGE.buildbin-libdir MiRaGE_1.4.0.tar.gz >MiRaGE-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=MiRaGE.buildbin-libdir --install="check:MiRaGE-install.out" --force-multiarch --no-vignettes --timings MiRaGE_1.4.0.tar.gz && mv MiRaGE.buildbin-libdir/* MiRaGE.Rcheck/ && rmdir MiRaGE.buildbin-libdir

StartedAt: 2014-04-05 05:10:43 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:13:32 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 168.9 seconds

RetCode: 0

Status:  OK

CheckDir: MiRaGE.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/MiRaGE.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 'MiRaGE/DESCRIPTION' ... OK
* this is package 'MiRaGE' version '1.4.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/doc/.goutputstream-0CTGCW
  inst/doc/.goutputstream-E9SXCW
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MiRaGE' 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
Package in Depends field not imported from: 'Biobase'
  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
TBL2_HS_gen: no visible global function definition for
  'read.DNAStringSet'
TBL2_HS_gen: no visible global function definition for
  'read.RNAStringSet'
TBL2_MM_gen: no visible global function definition for
  'read.DNAStringSet'
TBL2_MM_gen: no visible global function definition for
  'read.RNAStringSet'
getMiRaGEData: no visible global function definition for 'biocLite'
getMiRaGEData: no visible binding for global variable 'TBL2'
getMiRaGEData: no visible binding for global variable 'id_conv'
getMiRaGEData: no visible binding for global variable 'conv_id'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'MiRaGE.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
MiRaGE        13.58   0.20   14.18
getMiRaGEData  5.72   0.17    5.90
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
MiRaGE        15.69   0.45   16.16
getMiRaGEData  7.47   0.23    7.70
* 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 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/MiRaGE.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MiRaGE' ...
** R
** data
** 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 'MiRaGE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MiRaGE' as MiRaGE_1.4.0.zip
* DONE (MiRaGE)

name	user	system	elapsed
HS_conv_id	0.08	0.00	0.08
MM_conv_id	0	0	0
MiRaGE	13.58	0.20	14.18
TBL2_HS_gen	0	0	0
TBL2_MM_gen	0	0	0
getMiRaGEData	5.72	0.17	5.90
id_conv_gen	0	0	0

name	user	system	elapsed
HS_conv_id	0.11	0.00	0.11
MM_conv_id	0	0	0
MiRaGE	15.69	0.45	16.16
TBL2_HS_gen	0	0	0
TBL2_MM_gen	0	0	0
getMiRaGEData	7.47	0.23	7.70
id_conv_gen	0	0	0