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CHECK report for safe on celaya2

This page was generated on 2019-10-16 12:45:22 -0400 (Wed, 16 Oct 2019).

Package 1446/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
safe 3.24.0
William T. Barry
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/safe
Branch: RELEASE_3_9
Last Commit: dfc648f
Last Changed Date: 2019-05-02 11:53:04 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: safe
Version: 3.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:safe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings safe_3.24.0.tar.gz
StartedAt: 2019-10-16 06:31:56 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 06:34:00 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 124.3 seconds
RetCode: 0
Status:  OK 
CheckDir: safe.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:safe.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings safe_3.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/safe.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘safe/DESCRIPTION’ ... OK
* this is package ‘safe’ version ‘3.24.0’
* 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 787Kb to 391Kb
  consider running tools::compactPDF() on these files
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/safe.Rcheck/00check.log’
for details.



Installation output

safe.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL safe
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘safe’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (safe)

Tests output


Example timings

safe.Rcheck/safe-Ex.timings

nameusersystemelapsed
getCmatrix0.0020.0010.003
safe0.2690.0810.350
safeplot0.2330.0710.305