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CHECK report for pathifier on tokay2

This page was generated on 2019-04-09 12:06:03 -0400 (Tue, 09 Apr 2019).

Package 1149/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathifier 1.21.0
Assif Yitzhaky
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/pathifier
Branch: master
Last Commit: 7cdb166
Last Changed Date: 2018-10-30 11:54:31 -0400 (Tue, 30 Oct 2018)
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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: pathifier
Version: 1.21.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pathifier_1.21.0.tar.gz
StartedAt: 2019-04-09 04:47:19 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:48:57 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 97.7 seconds
RetCode: 0
Status:  OK  
CheckDir: pathifier.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pathifier_1.21.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pathifier.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pathifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathifier' version '1.21.0'
* 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 'pathifier' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getpathway: no visible global function definition for 'var'
.samplings_stdev: no visible binding for global variable 'sd'
.score_pathway: no visible binding for global variable 'sd'
.score_pathway: no visible global function definition for 'aggregate'
.score_pathway: no visible global function definition for 'dist'
quantify_pathways_deregulation: no visible binding for global variable
  'sd'
quantify_pathways_deregulation: no visible global function definition
  for 'prcomp'
Undefined global functions or variables:
  aggregate dist prcomp sd var
Consider adding
  importFrom("stats", "aggregate", "dist", "prcomp", "sd", "var")
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
Examples with CPU or elapsed time > 5s
                                user system elapsed
pathifier-package              15.69   0.11   15.94
quantify_pathways_deregulation 12.50   0.03   12.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
pathifier-package              13.63   0.04   16.47
quantify_pathways_deregulation 11.61   0.02   11.66
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/pathifier.Rcheck/00check.log'
for details.



Installation output

pathifier.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/pathifier_1.21.0.tar.gz && rm -rf pathifier.buildbin-libdir && mkdir pathifier.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathifier.buildbin-libdir pathifier_1.21.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL pathifier_1.21.0.zip && rm pathifier_1.21.0.tar.gz pathifier_1.21.0.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 1864k  100 1864k    0     0  4486k      0 --:--:-- --:--:-- --:--:-- 4559k

install for i386

* installing *source* package 'pathifier' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pathifier'
    finding HTML links ... done
    KEGG                                    html  
    Sheffer                                 html  
    pathifier-package                       html  
    quantify_pathways_deregulation          html  
** 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

install for x64

* installing *source* package 'pathifier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathifier' as pathifier_1.21.0.zip
* DONE (pathifier)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'pathifier' successfully unpacked and MD5 sums checked

Tests output


Example timings

pathifier.Rcheck/examples_i386/pathifier-Ex.timings

nameusersystemelapsed
KEGG0.040.000.03
Sheffer0.030.000.03
pathifier-package15.69 0.1115.94
quantify_pathways_deregulation12.50 0.0312.58

pathifier.Rcheck/examples_x64/pathifier-Ex.timings

nameusersystemelapsed
KEGG0.030.000.03
Sheffer0.030.000.03
pathifier-package13.63 0.0416.47
quantify_pathways_deregulation11.61 0.0211.66