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BioC experimental data: CHECK report for faahKO on malbec2

This page was generated on 2017-08-15 15:07:44 -0400 (Tue, 15 Aug 2017).

Package 91/316HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
faahKO 1.16.0
Colin A. Smith
Snapshot Date: 2017-08-15 09:00:06 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_5/experiment/pkgs/faahKO
Last Changed Rev: 4155 / Revision: 4227
Last Changed Date: 2017-04-24 16:09:26 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: faahKO
Version: 1.16.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings faahKO_1.16.0.tar.gz
StartedAt: 2017-08-15 10:41:27 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 10:44:04 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 156.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: faahKO.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings faahKO_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/faahKO.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.16.0’
* 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 ... 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-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
faahko2.8240.2403.093