Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-04-13 12:07:03 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for pathifier on tokay2


To the developers/maintainers of the pathifier package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathifier.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1375/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathifier 1.32.0  (landing page)
Assif Yitzhaky
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/pathifier
git_branch: RELEASE_3_14
git_last_commit: 40c6b3c
git_last_commit_date: 2021-10-26 12:08:35 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pathifier
Version: 1.32.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pathifier_1.32.0.tar.gz
StartedAt: 2022-04-13 00:17:04 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 00:18:52 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 108.0 seconds
RetCode: 0
Status:   OK  
CheckDir: pathifier.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathifier.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings pathifier_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/pathifier.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.32.0'
* 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 (user + system) or elapsed time > 5s
                                user system elapsed
pathifier-package              17.51   0.05   19.23
quantify_pathways_deregulation 15.41   0.01   17.49
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
pathifier-package              12.14   0.00   12.83
quantify_pathways_deregulation 11.07   0.01   11.09
* 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-3.14-bioc/meat/pathifier.Rcheck/00check.log'
for details.



Installation output

pathifier.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/pathifier_1.32.0.tar.gz && rm -rf pathifier.buildbin-libdir && mkdir pathifier.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathifier.buildbin-libdir pathifier_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL pathifier_1.32.0.zip && rm pathifier_1.32.0.tar.gz pathifier_1.32.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 26 1866k   26  491k    0     0   821k      0  0:00:02 --:--:--  0:00:02  822k
100 1866k  100 1866k    0     0  1284k      0  0:00:01  0:00:01 --:--:-- 1285k

install for i386

* installing *source* package 'pathifier' ...
** using staged installation
** 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_1.32.0.zip
* DONE (pathifier)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'pathifier' successfully unpacked and MD5 sums checked

Tests output


Example timings

pathifier.Rcheck/examples_i386/pathifier-Ex.timings

nameusersystemelapsed
KEGG0.030.000.03
Sheffer0.040.000.04
pathifier-package17.51 0.0519.23
quantify_pathways_deregulation15.41 0.0117.49

pathifier.Rcheck/examples_x64/pathifier-Ex.timings

nameusersystemelapsed
KEGG0.010.020.03
Sheffer0.050.000.05
pathifier-package12.14 0.0012.83
quantify_pathways_deregulation11.07 0.0111.09