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CHECK report for HTSanalyzeR on tokay2

This page was generated on 2019-04-09 11:58:24 -0400 (Tue, 09 Apr 2019).

Package 759/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HTSanalyzeR 2.35.1
Xin Wang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/HTSanalyzeR
Branch: master
Last Commit: 2ae206c
Last Changed Date: 2019-01-04 13:35:31 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: HTSanalyzeR
Version: 2.35.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HTSanalyzeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HTSanalyzeR_2.35.1.tar.gz
StartedAt: 2019-04-09 03:31:09 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:36:58 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 348.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: HTSanalyzeR.Rcheck
Warnings: 1

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:HTSanalyzeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HTSanalyzeR_2.35.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/HTSanalyzeR.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 'HTSanalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSanalyzeR' version '2.35.1'
* 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 'HTSanalyzeR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/GSCA-class.Rd:112: file link 'writeHits' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:8: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:9: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:207: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:218: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:218: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:18: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:27: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:28: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:32: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:10: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:13: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:23: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:28: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:69: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:81: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:13: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:26: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:30: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:14: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:24: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:29: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotSubNet.Rd:10: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotSubNet.Rd:23: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotSubNet.Rd:24: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotSubNet.Rd:28: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:11: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:11: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:15: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:20: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:30: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:31: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:35: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:35: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:112: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:113: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:11: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:11: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:15: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:15: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:25: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:26: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:26: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:30: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:30: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:69: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/report.Rd:70: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/reportAll.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/reportAll.Rd:10: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/reportAll.Rd:14: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/reportAll.Rd:14: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/reportAll.Rd:24: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/reportAll.Rd:27: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/reportAll.Rd:31: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/reportAll.Rd:31: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:14: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:14: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:18: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:18: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:28: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:28: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:29: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:29: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:33: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:33: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:44: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/summarize.Rd:49: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewEnrichMap.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewEnrichMap.Rd:13: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewEnrichMap.Rd:24: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewEnrichMap.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewEnrichMap.Rd:29: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewGSEA.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewGSEA.Rd:14: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewGSEA.Rd:24: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewGSEA.Rd:27: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewSubNet.Rd:10: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewSubNet.Rd:20: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/viewSubNet.Rd:25: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/writeReportHTSA.Rd:8: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/writeReportHTSA.Rd:8: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/writeReportHTSA.Rd:17: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/writeReportHTSA.Rd:20: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/writeReportHTSA.Rd:56: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/writeReportHTSA.Rd:57: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
  Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/HTSanalyzeR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'igraph'
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls in package code:
  'org.Ce.eg.db' 'org.Dm.eg.db' 'org.Hs.eg.db' 'org.Mm.eg.db'
  'org.Rn.eg.db'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'HTSanalyzeR/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("/////////////////////////////////////////////////////////////////////////////\n\n//------------------    Thanks for using HTSanalyzeR    -------------------//\n \n//------------please use function changes() to see new changes-------------//\n\n//------------please report any bug to [email protected]//\n\n/////////////////////////////////////////////////////////////////////////////\n",     appendLF = FALSE)

See section 'Good practice' in '?.onAttach'.

appendGSTerms,GSCA : appendKEGGTerm: warning in mget(gsKEGG, env =
  KEGGPATHID2NAME, ifnotfound = NA): partial argument match of 'env' to
  'envir'
HTSanalyzeR4cellHTS2: no visible global function definition for 'fData'
HTSanalyzeR4cellHTS2: no visible global function definition for 'new'
KeggGeneSets: no visible binding for global variable 'KEGGPATHID2EXTID'
aggregatePvals: no visible global function definition for 'is'
aggregatePvals: no visible global function definition for 'pchisq'
aggregatePvals : <anonymous>: no visible global function definition for
  'pnorm'
aggregatePvals : <anonymous>: no visible global function definition for
  'qnorm'
aggregatePvals: no visible global function definition for 'p.adjust'
analyzeGeneSetCollections: no visible global function definition for
  'p.adjust'
biogridDataDownload: no visible global function definition for
  'download.file'
biogridDataDownload: no visible global function definition for 'unzip'
biogridDataDownload: no visible global function definition for
  'read.table'
cellHTS2OutputStatTests: no visible global function definition for
  'fData'
cellHTS2OutputStatTests: no visible global function definition for
  'median'
cellHTS2OutputStatTests : <anonymous>: no visible global function
  definition for 't.test'
cellHTS2OutputStatTests : <anonymous>: no visible global function
  definition for 'wilcox.test'
collectionGsea: no visible global function definition for 'is'
collectionGsea: no visible global function definition for
  'txtProgressBar'
collectionGsea: no visible global function definition for
  'setTxtProgressBar'
drosoAnnotationConvertor: no visible global function definition for
  'is'
gseaPlots: no visible global function definition for 'par'
gseaPlots: no visible global function definition for 'plot'
gseaPlots: no visible global function definition for 'abline'
gseaPlots: no visible global function definition for 'lines'
gseaScoresBatchParallel: no visible global function definition for
  'parSapply'
hyperGeoTest: no visible global function definition for 'phyper'
makeGSEAplots: no visible global function definition for 'pdf'
makeGSEAplots: no visible global function definition for 'png'
makeGSEAplots: no visible global function definition for 'dev.off'
makeOverlapTable: no visible global function definition for
  'write.table'
mammalAnnotationConvertor: no visible global function definition for
  'is'
multiHyperGeoTest: no visible global function definition for
  'txtProgressBar'
multiHyperGeoTest : <anonymous>: no visible global function definition
  for 'setTxtProgressBar'
multiHyperGeoTest: no visible global function definition for 'p.adjust'
networkPlot: no visible global function definition for 'is'
networkPlot: no visible global function definition for
  'colorRampPalette'
networkPlot: no visible global function definition for 'points'
networkPlot: no visible global function definition for 'text'
pairwiseGsea: no visible global function definition for 'p.adjust'
pairwiseGseaPlot: no visible global function definition for 'pdf'
pairwiseGseaPlot: no visible global function definition for 'png'
pairwiseGseaPlot: no visible global function definition for 'par'
pairwiseGseaPlot: no visible global function definition for 'plot'
pairwiseGseaPlot: no visible global function definition for 'abline'
pairwiseGseaPlot: no visible global function definition for 'dev.off'
pairwisePhenoMannWhit : <anonymous>: no visible global function
  definition for 'wilcox.test'
pairwisePhenoMannWhit: no visible global function definition for
  'p.adjust'
paraCheck: no visible global function definition for 'is'
writeReportHTSA: no visible global function definition for 'is'
writeReportHTSA: no visible global function definition for
  'write.table'
appendGSTerms,GSCA : appendKEGGTerm: no visible binding for global
  variable 'KEGGPATHID2NAME'
plotEnrichMap,GSCA: no visible global function definition for 'pdf'
plotEnrichMap,GSCA: no visible global function definition for 'png'
plotEnrichMap,GSCA: no visible global function definition for 'dev.off'
plotSubNet,NWA: no visible global function definition for 'pdf'
plotSubNet,NWA: no visible global function definition for 'png'
plotSubNet,NWA: no visible global function definition for 'dev.off'
viewEnrichMap,GSCA: no visible global function definition for
  'colorRampPalette'
viewEnrichMap,GSCA: no visible global function definition for 'grey'
viewEnrichMap,GSCA: no visible global function definition for 'title'
viewEnrichMap,GSCA: no visible global function definition for 'points'
viewEnrichMap,GSCA: no visible global function definition for 'text'
Undefined global functions or variables:
  KEGGPATHID2EXTID KEGGPATHID2NAME abline colorRampPalette dev.off
  download.file fData grey is lines median new p.adjust par parSapply
  pchisq pdf phyper plot png pnorm points qnorm read.table
  setTxtProgressBar t.test text title txtProgressBar unzip wilcox.test
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "grey", "pdf",
             "png")
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "median", "p.adjust", "pchisq", "phyper", "pnorm",
             "qnorm", "t.test", "wilcox.test")
  importFrom("utils", "download.file", "read.table", "setTxtProgressBar",
             "txtProgressBar", "unzip", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
GOGeneSets  1.6   0.08      22
** running examples for arch 'x64' ... OK
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/HTSanalyzeR.Rcheck/00check.log'
for details.

Installation output

HTSanalyzeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/HTSanalyzeR_2.35.1.tar.gz && rm -rf HTSanalyzeR.buildbin-libdir && mkdir HTSanalyzeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HTSanalyzeR.buildbin-libdir HTSanalyzeR_2.35.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL HTSanalyzeR_2.35.1.zip && rm HTSanalyzeR_2.35.1.tar.gz HTSanalyzeR_2.35.1.zip
###
##############################################################################
##############################################################################


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100 2651k  100 2651k    0     0  28.1M      0 --:--:-- --:--:-- --:--:-- 30.8M

install for i386

* installing *source* package 'HTSanalyzeR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** help
*** installing help indices
  converting help for package 'HTSanalyzeR'
    finding HTML links ... done
    FDRcollectionGsea                       html  
    GOGeneSets                              html  
    GSCA-class                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/GSCA-class.Rd:112: file link 'writeHits' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    GenHTSAHtmlRowUnit                      html  
    HTSanalyzeR                             html  
    HTSanalyzeR4cellHTS2                    html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:8: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:9: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:207: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:218: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:218: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    KeggGeneSets                            html  
    NWA-class                               html  
    aggregatePvals                          html  
    analyze                                 html  
    analyzeGeneSetCollections               html  
    annotationConvertor                     html  
    appendGSTerms                           html  
    biogridDataDownload                     html  
    celAnnotationConvertor                  html  
    cellHTS2OutputStatTests                 html  
    changes                                 html  
    collectionGsea                          html  
    data-KcViab                             html  
    drosoAnnotationConvertor                html  
    duplicateRemover                        html  
    getTopGeneSets                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:18: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:27: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:28: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/getTopGeneSets.Rd:32: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    gseaPlots                               html  
    gseaScores                              html  
    htmlAttrVectorPaste                     html  
    hyperGeoTest                            html  
    interactome                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:10: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:13: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:23: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:28: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:69: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/interactome.Rd:81: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    makeGSEAplots                           html  
    makeOverlapTable                        html  
    mammalAnnotationConvertor               html  
    multiHyperGeoTest                       html  
    networkAnalysis                         html  
    networkPlot                             html  
    pairwiseGsea                            html  
    pairwiseGseaPlot                        html  
    pairwisePhenoMannWhit                   html  
    paraCheck                               html  
    permutationPvalueCollectionGsea         html  
    plotEnrichMap                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:13: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:26: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotEnrichMap.Rd:30: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    plotGSEA                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:10: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:14: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:24: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:25: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotGSEA.Rd:29: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    plotSubNet                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotSubNet.Rd:10: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotSubNet.Rd:23: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotSubNet.Rd:24: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/plotSubNet.Rd:28: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
    preprocess                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:11: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:11: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:15: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:20: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:30: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:31: file link 'NWA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpukFico/R.INSTALL215c130a31f3/HTSanalyzeR/man/preprocess.Rd:35: file link 'GSCA' in package 'HTSanalyzeR' does not exist and so has been treated as a topic
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    report                                  html  
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    reportAll                               html  
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    summarize                               html  
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    viewEnrichMap                           html  
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    viewGSEA                                html  
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    viewSubNet                              html  
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    writeHTSAHtmlHead                       html  
    writeHTSAHtmlSummary                    html  
    writeHTSAHtmlTab                        html  
    writeHTSAHtmlTable                      html  
    writeHTSAHtmlTail                       html  
    writeReportHTSA                         html  
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** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'HTSanalyzeR' ...
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
* MD5 sums
packaged installation of 'HTSanalyzeR' as HTSanalyzeR_2.35.1.zip
* DONE (HTSanalyzeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'HTSanalyzeR' successfully unpacked and MD5 sums checked

Tests output

Example timings

HTSanalyzeR.Rcheck/examples_i386/HTSanalyzeR-Ex.timings

nameusersystemelapsed
FDRcollectionGsea0.100.020.12
GOGeneSets 1.60 0.0822.00
GSCA-class000
HTSanalyzeR4cellHTS2000
KeggGeneSets2.440.062.50
NWA-class000
aggregatePvals000
analyze000
analyzeGeneSetCollections000
annotationConvertor0.640.000.64
appendGSTerms000
biogridDataDownload000
celAnnotationConvertor1.320.012.00
cellHTS2OutputStatTests000
changes000
collectionGsea0.170.020.19
data-KcViab1.400.061.47
drosoAnnotationConvertor1.470.031.50
duplicateRemover000
getTopGeneSets000
gseaPlots000
gseaScores000
hyperGeoTest2.060.022.07
interactome000
mammalAnnotationConvertor1.780.001.78
multiHyperGeoTest000
networkAnalysis000
networkPlot000
pairwiseGsea0.300.040.35
pairwiseGseaPlot000
pairwisePhenoMannWhit000
permutationPvalueCollectionGsea0.120.000.12
plotEnrichMap0.020.000.02
plotGSEA000
plotSubNet000
preprocess000
report000
reportAll000
summarize000
viewEnrichMap000
viewGSEA000
viewSubNet000
writeReportHTSA000

HTSanalyzeR.Rcheck/examples_x64/HTSanalyzeR-Ex.timings

nameusersystemelapsed
FDRcollectionGsea0.810.000.81
GOGeneSets1.810.151.97
GSCA-class000
HTSanalyzeR4cellHTS2000
KeggGeneSets2.640.042.67
NWA-class0.000.010.01
aggregatePvals000
analyze000
analyzeGeneSetCollections000
annotationConvertor0.560.000.57
appendGSTerms000
biogridDataDownload000
celAnnotationConvertor1.580.021.59
cellHTS2OutputStatTests000
changes000
collectionGsea0.840.000.85
data-KcViab1.020.001.01
drosoAnnotationConvertor0.810.020.83
duplicateRemover000
getTopGeneSets000
gseaPlots000
gseaScores0.020.000.01
hyperGeoTest2.670.002.68
interactome000
mammalAnnotationConvertor2.010.052.06
multiHyperGeoTest0.020.000.01
networkAnalysis000
networkPlot000
pairwiseGsea0.730.000.74
pairwiseGseaPlot000
pairwisePhenoMannWhit000
permutationPvalueCollectionGsea0.240.000.23
plotEnrichMap000
plotGSEA000
plotSubNet000
preprocess000
report000
reportAll000
summarize000
viewEnrichMap000
viewGSEA000
viewSubNet000
writeReportHTSA000