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CHECK report for safe on tokay2

This page was generated on 2018-10-17 08:32:24 -0400 (Wed, 17 Oct 2018).

Package 1306/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
safe 3.20.0
William T. Barry
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/safe
Branch: RELEASE_3_7
Last Commit: bd236e0
Last Changed Date: 2018-04-30 10:35:01 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: safe
Version: 3.20.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings safe_3.20.0.tar.gz
StartedAt: 2018-10-17 04:39:02 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:40:44 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 102.6 seconds
RetCode: 0
Status:  OK  
CheckDir: safe.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:safe.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings safe_3.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/safe.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'safe/DESCRIPTION' ... OK
* this is package 'safe' version '3.20.0'
* 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 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'
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/safe.Rcheck/00check.log'
for details.



Installation output

safe.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/safe_3.20.0.tar.gz && rm -rf safe.buildbin-libdir && mkdir safe.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=safe.buildbin-libdir safe_3.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL safe_3.20.0.zip && rm safe_3.20.0.tar.gz safe_3.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  164k  100  164k    0     0  2486k      0 --:--:-- --:--:-- --:--:-- 2791k

install for i386

* installing *source* package 'safe' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'safe'
    finding HTML links ... done
    SAFE-class                              html  
    gene.results                            html  
    getCmatrix                              html  
    p53.stat                                html  
    safe-internal                           html  
    safe-package                            html  
    safe                                    html  
    safe.toptable                           html  
    safedag                                 html  
    safeplot                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'safe' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'safe' as safe_3.20.0.zip
* DONE (safe)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'safe' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

safe.Rcheck/examples_i386/safe-Ex.timings

nameusersystemelapsed
getCmatrix000
safe0.270.030.29
safeplot0.110.000.11

safe.Rcheck/examples_x64/safe-Ex.timings

nameusersystemelapsed
getCmatrix000
safe0.310.020.33
safeplot0.110.000.11