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BioC experimental data: CHECK report for Fletcher2013b on zin2

This page was generated on 2015-10-07 16:20:59 -0700 (Wed, 07 Oct 2015).

Package 84/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Fletcher2013b 1.4.0
Mauro Castro
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/Fletcher2013b
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 [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Fletcher2013b
Version: 1.4.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Fletcher2013b_1.4.0.tar.gz
StartedAt: 2015-10-07 09:44:28 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 09:50:58 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 390.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Fletcher2013b.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Fletcher2013b_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-data-experiment/meat/Fletcher2013b.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 ‘Fletcher2013b/DESCRIPTION’ ... OK
* this is package ‘Fletcher2013b’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Fletcher2013b’ can be installed ... [12s/37s] OK
* checking installed package size ... NOTE
  installed size is 265.9Mb
  sub-directories of 1Mb or more:
    data  262.0Mb
    doc     3.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Fletcher2013gsea.regulons: no visible global function definition for
  ‘tna.gsea1’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘tni.dpi.filter’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘graph.adjacency’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘get.edgelist’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘E’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘E<-’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘V’
Fletcher2013pipeline.consensusnet: no visible global function
  definition for ‘V<-’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘tni.get’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘graph.adjacency’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘V’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘V<-’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘E’
Fletcher2013pipeline.enrichmap: no visible global function definition
  for ‘E<-’
Fletcher2013pipeline.mra1st: no visible global function definition for
  ‘tni.dpi.filter’
Fletcher2013pipeline.mra2nd: no visible global function definition for
  ‘tni.dpi.filter’
Fletcher2013pipeline.mraNormals: no visible global function definition
  for ‘tni.dpi.filter’
Fletcher2013pipeline.mraTALL: no visible global function definition for
  ‘tni.dpi.filter’
draw2venn: no visible global function definition for ‘gpar’
draw2venn: no visible global function definition for ‘textGrob’
draw2venn: no visible global function definition for ‘linesGrob’
getTSSmap: no visible global function definition for ‘listDatasets’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/25s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
rtni.data 3.334  0.096   8.623
* 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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-data-experiment/meat/Fletcher2013b.Rcheck/00check.log’
for details.


Fletcher2013b.Rcheck/00install.out:

* installing *source* package ‘Fletcher2013b’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (Fletcher2013b)

Fletcher2013b.Rcheck/Fletcher2013b-Ex.timings:

nameusersystemelapsed
Fletcher2013b.gsea.regulons0.0000.0000.001
Fletcher2013b.pipelines0.0000.0000.001
miscellaneous0.7040.0021.968
rtni.data3.3340.0968.623
siRNA0.0070.0000.007