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CHECK report for SBGNview.data on riesling1

This page was generated on 2021-01-21 16:01:38 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE SBGNview.data PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 321/386HostnameOS / ArchINSTALLBUILDCHECK
SBGNview.data 1.5.0
Xiaoxi Dong
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/SBGNview.data
Branch: master
Last Commit: 6f92739
Last Changed Date: 2020-10-27 10:30:31 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: SBGNview.data
Version: 1.5.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBGNview.data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SBGNview.data_1.5.0.tar.gz
StartedAt: 2021-01-21 11:46:08 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:47:55 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 107.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SBGNview.data.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SBGNview.data.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings SBGNview.data_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/SBGNview.data.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SBGNview.data/DESCRIPTION' ... OK
* this is package 'SBGNview.data' version '1.5.0'
* 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 'SBGNview.data' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 61.8Mb
  sub-directories of 1Mb or more:
    data  61.7Mb
* 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 ... OK
* 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 ... WARNING
  Warning: found non-ASCII strings
  '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
  <sbgn xmlns="http://sbgn.org/libsbgn/pd/0.1">
      <map>
          <glyph id="glyph0" class="compartment">
              <label text="vacuole">
                  <bbox y="56.0" x="203.5" h="16.0" w="51.0"/>
              </label>
              <bbox y="50.0" x="50.0" h="529.0" w="358.0"/>
          </glyph>
          <glyph id="glyph8" class="simple chemical">
              <label text="sucrose"/>
              <clone/>
              <bbox y="80.5" x="205.25" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph13" class="simple chemical">
              <label text="D-glucose"/>
              <clone/>
              <bbox y="200.5" x="262.0" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph10" class="simple chemical">
              <label text="[beta-D-fructosyl-(2<e2><86><92>1)-]m"/>
              <bbox y="399.5" x="210.0" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph5" class="simple chemical">
              <label text="[beta-D-fructosyl-(2<e2><86><92>1)-]n"/>
              <bbox y="429.5" x="285.0" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph15" class="simple chemical">
              <label text="[beta-D-fructosyl-(2<e2><86><92>1)-]m-1"/>
              <bbox y="505.0" x="285.0" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph14" class="simple chemical">
              <label text="[beta-D-fructosyl-(2<e2><86><92>1)-]n+1"/>
              <bbox y="535.0" x="210.0" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph16" class="simple chemical">
              <label text="D-glucose"/>
              <clone/>
              <bbox y="327.5" x="316.0" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph6" class="simple chemical">
              <label text="sucrose"/>
              <clone/>
              <bbox y="250.5" x="322.0" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph12" class="simple chemical">
              <label text="bifurcose"/>
              <bbox y="348.5" x="265.75" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph9" class="simple chemical">
              <label text="sucrose"/>
              <clone/>
              <bbox y="250.5" x="92.0" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph7" class="simple chemical">
              <label text="neokestose"/>
              <bbox y="348.5" x="153.5" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph11" class="simple chemical">
              <label text="1(F)-beta-D-fructosylsucrose"/>
              <bbox y="226.5" x="205.25" h="30.0" w="30.0"/>
          </glyph>
          <glyph id="glyph1" class="macromolecule">
              <label text="2.4.1.99"/>
              <bbox y="168.5" x="131.25" h="30.0" w="54.0"/>
          </glyph>
          <glyph id="glyph17" orientation="vertical" class="process">
              <bbox y="178.5" x="215.25" h="10.0" w="10.0"/>
              <port y="173.5" x="220.25" id="glyph17.1"/>
              <port y="193.5" x="220.25" id="glyph17.2"/>
          </glyph>
          <glyph id="glyph3" class="macromolecule">
              <label text="2.4.1.100"/>
              <bbox y="469.5" x="136.0" h="30.0" w="54.0"/>
          </glyph>
          <glyph id="glyph20" orientation="vertical" class="process">
              <bbox y="479.5" x="220.0" h="10.0" w="10.0"/>
              <port y="474.5" x="225.0" id="glyph20.1"/>
              <port y="494.5" x="225.0" id="glyph20.2"/>
          </glyph>
          <glyph id="glyph2" class="macromolecule">
              <label text="2.4.1.-"/>
              <bbox y="287.25" x="79.5" h="30.0" w="54.0"/>
          </glyph>
          <glyph id="glyph19" orientation="vertical" class="process">
              <bbox y="297.25" x="163.5" h="10.0" w="10.0"/>
              <port y="292.25" x="168.5" id="glyph19.1"/>
              <port y="312.25" x="168.5" id="glyph19.2"/>
          </glyph>
          <glyph id="glyph4" class="macromolecule">
              <label text="2.4.1.10"/>
              <bbox y="287.25" x="191.75" h="30.0" w="54.0"/>
          </glyph>
          <glyph id="glyph18" orientation="vertical" class="process">
              <bbox y="297.25" x="275.75" h="10.0" w="10.0"/>
              <port y="312.25" x="280.75" id="glyph18.2"/>
              <port y="292.25" x="280.75" id="glyph18.1"/>
          </glyph>
          <arc target="glyph8" source="glyph17.1" class="production">
              <glyph id="glyph21" class="stoichiometry">
                  <label text="2"/>
                  <bbox y="121.0" x="207.0" h="17.5" w="21.5"/>
              </glyph>
              <start y="173.5" x="220.25"/>
              <end y="110.5" x="220.25"/>
          </arc>
          <arc target="glyph13" source="glyph17.2" class="production">
              <start y="193.5" x="220.25"/>
              <end y="208.13242" x="263.93405"/>
          </arc>
          <arc target="glyph10" source="glyph20.1" class="production">
              <start y="474.5" x="225.0"/>
              <end y="429.5" x="225.0"/>
          </arc>
          <arc target="glyph5" source="glyph20.1" class="production">
              <start y="474.5" x="225.0"/>
              <end y="450.07086" x="286.07285"/>
          </arc>
          <arc target="glyph15" source="glyph20.2" class="production">
              <start y="494.5" x="225.0"/>
              <end y="513.5826" x="286.44208"/>
          </arc>
          <arc target="glyph14" source="glyph20.2" class="production">
              <start y="494.5" x="225.0"/>
              <end y="535.0" x="225.0"/>
          </arc>
          <arc target="glyph16" source="glyph18.2" class="production">
              <start y="312.25" x="280.75"/>
              <end y="333.12247" x="319.29266"/>
          </arc>
          <arc target="glyph6" source="glyph18.1" class="production">
              <start y="292.25" x="280.75"/>
              <end y="271.942" x="323.45377"/>
          </arc>
          <arc target="glyph12" source="glyph18.2" class="production">
              <start y="312.25" x="280.75"/>
              <end y="348.5" x="280.75"/>
          </arc>
          <arc target="glyph9" source="glyph19.1" class="production">
              <start y="292.25" x="168.5"/>
              <end y="271.48294" x="120.755165"/>
          </arc>
          <arc target="glyph7" source="glyph19.2" class="production">
              <start y="312.25" x="168.5"/>
              <end y="348.5" x="168.5"/>
          </arc>
          <arc target="glyph11" source="glyph17.2" class="production">
              <start y="193.5" x="220.25"/>
              <end y="226.5" x="220.25"/>
          </arc>
          <arc target="glyph11" source="glyph18.1" class="production">
              <start y="292.25" x="280.75"/>
              <end y="251.14008" x="231.74213"/>
          </arc>
          <arc target="glyph11" source="glyph19.1" class="production">
              <start y="292.25" x="168.5"/>
              <end y="252.00262" x="209.54044"/>
          </arc>
          <arc target="glyph17" source="glyph1" class="catalysis">
              <start y="183.5" x="185.25"/>
              <end y="183.5" x="215.25"/>
          </arc>
          <arc target="glyph20" source="glyph3" class="catalysis">
              <start y="484.5" x="190.0"/>
              <end y="484.5" x="220.0"/>
          </arc>
          <arc target="glyph19" source="glyph2" class="catalysis">
              <start y="302.25" x="133.5"/>
              <end y="302.25" x="163.5"/>
          </arc>
          <arc target="glyph18" source="glyph4" class="catalysis">
              <start y="302.25" x="245.75"/>
              <end y="302.25" x="275.75"/>
          </arc>
      </map>
  </sbgn>
  ' in object 'sbgn.xmls'
  '<ff><d8><ff><e0>' in object 'sbgn.xmls'
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* 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 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/SBGNview.data.Rcheck/00check.log'
for details.



Installation output

SBGNview.data.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/SBGNview.data_1.5.0.tar.gz && rm -rf SBGNview.data.buildbin-libdir && mkdir SBGNview.data.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SBGNview.data.buildbin-libdir SBGNview.data_1.5.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SBGNview.data_1.5.0.zip && rm SBGNview.data_1.5.0.tar.gz SBGNview.data_1.5.0.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
  1 60.8M    1  848k    0     0  5808k      0  0:00:10 --:--:--  0:00:10 5769k
100 60.8M  100 60.8M    0     0  87.4M      0 --:--:-- --:--:-- --:--:-- 87.4M

install for i386

* installing *source* package 'SBGNview.data' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SBGNview.data'
    finding HTML links ... done
    IFNg                                    html  
REDIRECT:topic	 IFNg -> IFNg.html [ SUCCESS ]
    cancer.ds                               html  
REDIRECT:topic	 cancer.ds -> cancer.ds.html [ SUCCESS ]
    mapping                                 html  
REDIRECT:topic	 mapping -> mapping.html [ SUCCESS ]
REDIRECT:topic	 ENZYME_pathway.id -> mapping.html [ SUCCESS ]
REDIRECT:topic	 hsa_KO_ENTREZID -> mapping.html [ SUCCESS ]
REDIRECT:topic	 hsa_pathwayCommons_ENTREZID -> mapping.html [ SUCCESS ]
REDIRECT:topic	 mmu_KO_ENSEMBL -> mapping.html [ SUCCESS ]
REDIRECT:topic	 chebi_pathway.id -> mapping.html [ SUCCESS ]
REDIRECT:topic	 mmu_KO_ENTREZID -> mapping.html [ SUCCESS ]
REDIRECT:topic	 chebi_CompoundName -> mapping.html [ SUCCESS ]
REDIRECT:topic	 CompoundName_pathwayCommons -> mapping.html [ SUCCESS ]
REDIRECT:topic	 kegg.ligand_pathwayCommons -> mapping.html [ SUCCESS ]
REDIRECT:topic	 hsa_pathwayCommons_ENSEMBL -> mapping.html [ SUCCESS ]
REDIRECT:topic	 mmu_pathwayCommons_ENTREZID -> mapping.html [ SUCCESS ]
REDIRECT:topic	 KO_pathway.id -> mapping.html [ SUCCESS ]
REDIRECT:topic	 KO_pathwayCommons -> mapping.html [ SUCCESS ]
REDIRECT:topic	 SYMBOL_pathway.id -> mapping.html [ SUCCESS ]
REDIRECT:topic	 pathwayCommons_SYMBOL -> mapping.html [ SUCCESS ]
REDIRECT:topic	 chebi_pathwayCommons -> mapping.html [ SUCCESS ]
REDIRECT:topic	 mmu_pathwayCommons_ENSEMBL -> mapping.html [ SUCCESS ]
REDIRECT:topic	 hsa_ENTREZID_pathwayCommons -> mapping.html [ SUCCESS ]
    pathway.completeness.cutoff.info        html  
REDIRECT:topic	 pathway.completeness.cutoff.info -> pathway.completeness.cutoff.info.html [ SUCCESS ]
    pathway.species.pct_Mapped              html  
REDIRECT:topic	 pathway.species.pct_Mapped -> pathway.species.pct_Mapped.html [ SUCCESS ]
    sbgn.xmls                               html  
REDIRECT:topic	 sbgn.xmls -> sbgn.xmls.html [ SUCCESS ]
** 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 'SBGNview.data' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SBGNview.data' as SBGNview.data_1.5.0.zip
* DONE (SBGNview.data)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'SBGNview.data' successfully unpacked and MD5 sums checked

Tests output


Example timings