BioC experimental data: CHECK report for faahKO on morelia

Package: faahKO

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings faahKO_1.11.0.tar.gz

StartedAt: 2015-11-25 10:30:43 -0800 (Wed, 25 Nov 2015)

EndedAt: 2015-11-25 10:32:29 -0800 (Wed, 25 Nov 2015)

EllapsedTime: 105.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: faahKO.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings faahKO_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/faahKO.Rcheck’
* using R Under development (unstable) (2015-11-08 r69614)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘faahKO/DESCRIPTION’ ... OK
* this is package ‘faahKO’ version ‘1.11.0’
* 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 ... WARNING
Found the following file with a non-portable file name:
  inst/s_Proteomic profiling of yeast TFs.txt
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘faahKO’ can be installed ... [4s/32s] OK
* checking installed package size ... NOTE
  installed size is 42.7Mb
  sub-directories of 1Mb or more:
    cdf  42.4Mb
* 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
* 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 ‘xcms’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘xcms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘faahKO/R/zzz.R’:
  .onLoad calls:
    require(xcms)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.onLoad: warning in assign("faahko", faahko, env =
  getNamespace("faahKO")): partial argument match of 'env' to 'envir'
* 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 examples ... [3s/5s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-data-experiment/meat/faahKO.Rcheck/00check.log’
for details.

* installing *source* package ‘faahKO’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (faahKO)

name	user	system	elapsed
faahko	0.166	0.024	1.942