safe 3.6.1
William T. Barry
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/safe | | Last Changed Rev: 96552 / Revision: 102249 | | Last Changed Date: 2014-11-05 16:49:02 -0800 (Wed, 05 Nov 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### rm -rf safe.buildbin-libdir safe.Rcheck && mkdir safe.buildbin-libdir safe.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=safe.buildbin-libdir safe_3.6.1.tar.gz >safe.Rcheck\00install.out 2>&1 && cp safe.Rcheck\00install.out safe-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=safe.buildbin-libdir --install="check:safe-install.out" --force-multiarch --no-vignettes --timings safe_3.6.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/safe.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'safe/DESCRIPTION' ... OK
* this is package 'safe' version '3.6.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [6s] 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
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/safe.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'safe' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'safe' as safe_3.6.1.zip
* DONE (safe)