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This page was generated on 2021-06-17 12:05:29 -0400 (Thu, 17 Jun 2021).

CHECK results for EnrichmentBrowser on riesling1

To the developers/maintainers of the EnrichmentBrowser package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EnrichmentBrowser.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 554/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EnrichmentBrowser 2.23.0  (landing page)
Ludwig Geistlinger
Snapshot Date: 2021-06-16 14:50:06 -0400 (Wed, 16 Jun 2021)
URL: https://git.bioconductor.org/packages/EnrichmentBrowser
Branch: master
Last Commit: ef6c06d
Last Changed Date: 2021-05-19 12:07:36 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'KEGGgraph' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: EnrichmentBrowser
Version: 2.23.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EnrichmentBrowser.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings EnrichmentBrowser_2.23.0.tar.gz
StartedAt: 2021-06-16 23:55:07 -0400 (Wed, 16 Jun 2021)
EndedAt: 2021-06-17 00:01:47 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 400.2 seconds
RetCode: 0
Status:   OK  
CheckDir: EnrichmentBrowser.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EnrichmentBrowser.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings EnrichmentBrowser_2.23.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/EnrichmentBrowser.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EnrichmentBrowser/DESCRIPTION' ... OK
* this is package 'EnrichmentBrowser' version '2.23.0'
* package encoding: UTF-8
* 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 'EnrichmentBrowser' 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
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.exportToEnrichplot: no visible binding for global variable 'se'
.getGOFromBiomart: no visible binding for global variable
  'go_linkage_type'
.res2result: no visible binding for global variable 'se'
Undefined global functions or variables:
  go_linkage_type se
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
ebrowser    59.22   3.89   63.14
getGenesets 11.86   0.65   16.98
eaBrowse     6.31   0.75    7.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
ebrowser    55.98   4.70   60.68
getGenesets  9.46   0.53   14.10
eaBrowse     5.92   0.81    6.74
import       5.95   0.27    6.45
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/EnrichmentBrowser.Rcheck/00check.log'
for details.



Installation output

EnrichmentBrowser.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/EnrichmentBrowser_2.23.0.tar.gz && rm -rf EnrichmentBrowser.buildbin-libdir && mkdir EnrichmentBrowser.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EnrichmentBrowser.buildbin-libdir EnrichmentBrowser_2.23.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL EnrichmentBrowser_2.23.0.zip && rm EnrichmentBrowser_2.23.0.tar.gz EnrichmentBrowser_2.23.0.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
100  328k  100  328k    0     0  1231k      0 --:--:-- --:--:-- --:--:-- 1231k

install for i386

* installing *source* package 'EnrichmentBrowser' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EnrichmentBrowser'
    finding HTML links ... done
    combResults                             html  
    compileGRN                              html  
    finding level-2 HTML links ... done

    configEBrowser                          html  
    deAna                                   html  
    downloadPathways                        html  
    eaBrowse                                html  
    ebrowser                                html  
    export                                  html  
    getGenesets                             html  
    ggeaGraph                               html  
    idMap                                   html  
    import                                  html  
    isAvailable                             html  
    makeExampleData                         html  
    nbea                                    html  
    normalize                               html  
    plots                                   html  
    probe2gene                              html  
    readSE                                  html  
    sbea                                    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 'EnrichmentBrowser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EnrichmentBrowser' as EnrichmentBrowser_2.23.0.zip
* DONE (EnrichmentBrowser)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'EnrichmentBrowser' successfully unpacked and MD5 sums checked

Tests output


Example timings

EnrichmentBrowser.Rcheck/examples_i386/EnrichmentBrowser-Ex.timings

nameusersystemelapsed
combResults0.410.020.42
compileGRN3.170.203.37
configEBrowser000
deAna3.800.444.24
downloadPathways000
eaBrowse6.310.757.08
ebrowser59.22 3.8963.14
getGenesets11.86 0.6516.98
ggeaGraph3.980.054.03
idMap0.720.311.03
import4.730.164.89
isAvailable000
makeExampleData0.040.000.04
nbea0.210.000.21
normalize0.500.050.57
plots0.960.221.17
probe2gene0.060.000.06
readSE0.030.010.05
sbea0.190.000.19

EnrichmentBrowser.Rcheck/examples_x64/EnrichmentBrowser-Ex.timings

nameusersystemelapsed
combResults0.860.040.91
compileGRN3.250.223.47
configEBrowser000
deAna4.130.354.47
downloadPathways000
eaBrowse5.920.816.74
ebrowser55.98 4.7060.68
getGenesets 9.46 0.5314.10
ggeaGraph2.560.032.59
idMap0.670.331.00
import5.950.276.45
isAvailable000
makeExampleData0.030.000.04
nbea0.240.000.23
normalize0.500.090.59
plots0.950.111.08
probe2gene0.080.000.08
readSE0.050.000.05
sbea0.230.000.23