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BioC experimental data: CHECK report for faahKO on zin2

This page was generated on 2015-10-07 16:20:47 -0700 (Wed, 07 Oct 2015).

Package 75/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
faahKO 1.8.0
Colin A. Smith
Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/faahKO
Last Changed Rev: 3279 / Revision: 3442
Last Changed Date: 2015-04-16 13:16:53 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: faahKO
Version: 1.8.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings faahKO_1.8.0.tar.gz
StartedAt: 2015-10-07 09:40:36 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 09:42:09 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 92.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: faahKO.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings faahKO_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-data-experiment/meat/faahKO.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘faahKO/DESCRIPTION’ ... OK
* this is package ‘faahKO’ version ‘1.8.0’
* 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/8s] OK
* checking installed package size ... NOTE
  installed size is 42.8Mb
  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 ... [2s/4s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-data-experiment/meat/faahKO.Rcheck/00check.log’
for details.


faahKO.Rcheck/00install.out:

* 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)

faahKO.Rcheck/faahKO-Ex.timings:

nameusersystemelapsed
faahko0.1860.0110.394