safe 3.11.0 William T. Barry
Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/safe | Last Changed Rev: 109592 / Revision: 109826 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings safe_3.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/safe.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘safe/DESCRIPTION’ ... OK
* this is package ‘safe’ version ‘3.11.0’
* 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 ... [6s/6s] 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’
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
safe.express subGraph
* 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 798Kb to 402Kb
consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] 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-3.3-bioc/meat/safe.Rcheck/00check.log’
for details.