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BioC 3.4: CHECK report for safe on zin1

This page was generated on 2016-09-21 03:35:53 -0700 (Wed, 21 Sep 2016).

Package 1073/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
safe 3.13.0
William T. Barry
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/safe
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: safe
Version: 3.13.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings safe_3.13.0.tar.gz
StartedAt: 2016-09-20 12:14:33 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:15:31 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 57.8 seconds
RetCode: 0
Status:  OK 
CheckDir: safe.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings safe_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/safe.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘safe/DESCRIPTION’ ... OK
* this is package ‘safe’ version ‘3.13.0’
* 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 ‘safe’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ‘SparseM’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘GO.db’ ‘GOstats’ ‘PFAM.db’ ‘Rgraphviz’ ‘doRNG’ ‘foreach’
  ‘reactome.db’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
getCOXresiduals: no visible global function definition for ‘Surv’
getCOXresiduals: no visible global function definition for ‘coxph’
getCOXresiduals: no visible global function definition for ‘residuals’
getCmatrix: no visible binding for global variable ‘GOTERM’
safe: no visible binding for global variable ‘reactomeEXTID2PATHID’
safe: no visible global function definition for ‘safe.express’
safe: no visible global function definition for ‘getDoParWorkers’
safe: no visible global function definition for ‘%dorng%’
safe: no visible global function definition for ‘foreach’
safe.toptable: no visible binding for global variable ‘GOTERM’
safe.toptable: no visible binding for global variable ‘PFAMSCOP’
safe.toptable: no visible binding for global variable ‘reactome.db’
safedag: no visible binding for global variable ‘GOTERM’
safedag: no visible global function definition for ‘GOGraph’
safedag: no visible global function definition for ‘makeNodeAttrs’
safedag: no visible global function definition for ‘subGraph’
safedag: no visible global function definition for ‘agopen’
safeplot: no visible binding for global variable ‘GOTERM’
safeplot: no visible binding for global variable ‘PFAMID’
Undefined global functions or variables:
  %dorng% GOGraph GOTERM PFAMID PFAMSCOP Surv agopen coxph foreach
  getDoParWorkers makeNodeAttrs reactome.db reactomeEXTID2PATHID
  residuals safe.express subGraph
Consider adding
  importFrom("stats", "residuals")
to your NAMESPACE file.
* 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘SAFEmanual3.pdf’ from 797Kb to 381Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/safe.Rcheck/00check.log’
for details.


safe.Rcheck/00install.out:

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

safe.Rcheck/safe-Ex.timings:

nameusersystemelapsed
getCmatrix0.0040.0000.001
safe0.2400.0000.239
safeplot0.1240.0000.122