BioC 3.0: CHECK report for RMAPPER on moscato1

Package: RMAPPER

Version: 1.15.0

Command: rm -rf RMAPPER.buildbin-libdir && mkdir RMAPPER.buildbin-libdir && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RMAPPER.buildbin-libdir RMAPPER_1.15.0.tar.gz >RMAPPER-install.out 2>&1 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=RMAPPER.buildbin-libdir --install="check:RMAPPER-install.out" --force-multiarch --no-vignettes --timings RMAPPER_1.15.0.tar.gz && mv RMAPPER.buildbin-libdir/* RMAPPER.Rcheck/ && rmdir RMAPPER.buildbin-libdir

StartedAt: 2014-04-13 10:34:47 -0700 (Sun, 13 Apr 2014)

EndedAt: 2014-04-13 10:35:50 -0700 (Sun, 13 Apr 2014)

EllapsedTime: 62.4 seconds

RetCode: 0

Status:  OK

CheckDir: RMAPPER.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/RMAPPER.Rcheck'
* using R version 3.1.0 (2014-04-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RMAPPER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RMAPPER' version '1.15.0'
* 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 'RMAPPER' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'methods'
  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
readMAPPER: warning in read.delim(tc, sep = "\t", skip = 1, h = TRUE):
  partial argument match of 'h' to 'header'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [34s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
readMapper 0.05      0   31.17
** running examples for arch 'x64' ... [4s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/RMAPPER.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RMAPPER' ...
** 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 'RMAPPER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RMAPPER' as RMAPPER_1.15.0.zip
* DONE (RMAPPER)

name	user	system	elapsed
hits	0	0	0
mapperHits-class	0	0	0
query	0	0	0
readMapper	0.05	0.00	31.17
rmapperFactorTable	0.00	0.03	1.57
rmapperHelp	0.00	0.00	0.24

name	user	system	elapsed
hits	0	0	0
mapperHits-class	0	0	0
query	0	0	0
readMapper	0.05	0.00	1.68
rmapperFactorTable	0.00	0.01	1.11
rmapperHelp	0.00	0.00	0.31