Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:27 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 gsean on tokay2


To the developers/maintainers of the gsean package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gsean.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 836/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gsean 1.14.0  (landing page)
Dongmin Jung
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/gsean
git_branch: RELEASE_3_14
git_last_commit: b0c972b
git_last_commit_date: 2021-10-26 12:41:21 -0500 (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: gsean
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gsean.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gsean_1.14.0.tar.gz
StartedAt: 2022-01-20 21:03:24 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 21:08:07 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 283.4 seconds
RetCode: 0
Status:   OK  
CheckDir: gsean.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gsean.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gsean_1.14.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/gsean.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gsean/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gsean' version '1.14.0'
* 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 'gsean' 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
centrality_gsea: no visible global function definition for 'na.omit'
centrality_gsea: no visible global function definition for 'quantile'
exprs2adj: no visible global function definition for 'quantile'
label_prop_gsea: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit quantile
Consider adding
  importFrom("stats", "na.omit", "quantile")
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
centrality_gsea 1.08   0.06    5.11
label_prop_gsea 1.05   0.05    5.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
centrality_gsea 1.52   0.03    7.20
label_prop_gsea 1.39   0.06    6.47
gsean           0.86   0.25    6.77
* 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/gsean.Rcheck/00check.log'
for details.



Installation output

gsean.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/gsean_1.14.0.tar.gz && rm -rf gsean.buildbin-libdir && mkdir gsean.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gsean.buildbin-libdir gsean_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL gsean_1.14.0.zip && rm gsean_1.14.0.tar.gz gsean_1.14.0.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
 35  282k   35  101k    0     0   537k      0 --:--:-- --:--:-- --:--:--  536k
100  282k  100  282k    0     0  1074k      0 --:--:-- --:--:-- --:--:-- 1074k

install for i386

* installing *source* package 'gsean' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gsean'
    finding HTML links ... done
    GO_dme                                  html  
    KEGG_hsa                                html  
    centrality_gsea                         html  
    exprs2adj                               html  
    gsean-package                           html  
    gsean                                   html  
    label_prop_gsea                         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 'gsean' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gsean' as gsean_1.14.0.zip
* DONE (gsean)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'gsean' successfully unpacked and MD5 sums checked

Tests output


Example timings

gsean.Rcheck/examples_i386/gsean-Ex.timings

nameusersystemelapsed
GO_dme0.160.000.16
KEGG_hsa000
centrality_gsea1.080.065.11
exprs2adj3.940.714.64
gsean0.540.204.89
label_prop_gsea1.050.055.16

gsean.Rcheck/examples_x64/gsean-Ex.timings

nameusersystemelapsed
GO_dme0.110.000.11
KEGG_hsa0.010.000.02
centrality_gsea1.520.037.20
exprs2adj3.340.443.78
gsean0.860.256.77
label_prop_gsea1.390.066.47