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CHECK report for KEGGdzPathwaysGEO on malbec2

This page was generated on 2021-01-14 15:59:03 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE KEGGdzPathwaysGEO PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 192/385HostnameOS / ArchINSTALLBUILDCHECK
KEGGdzPathwaysGEO 1.29.0
Gaurav Bhatti
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO
Branch: master
Last Commit: 71b93f9
Last Changed Date: 2020-10-27 09:56:50 -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  OK 

Summary

Package: KEGGdzPathwaysGEO
Version: 1.29.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:KEGGdzPathwaysGEO.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings KEGGdzPathwaysGEO_1.29.0.tar.gz
StartedAt: 2021-01-14 12:19:48 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:25:11 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 322.1 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGdzPathwaysGEO.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:KEGGdzPathwaysGEO.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings KEGGdzPathwaysGEO_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/KEGGdzPathwaysGEO.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGdzPathwaysGEO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGdzPathwaysGEO’ version ‘1.29.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘KEGGdzPathwaysGEO’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 300.8Mb
  sub-directories of 1Mb or more:
    data  300.6Mb
* checking package 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
* 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
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘BiocGenerics’
  All declared Imports should be used.
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/KEGGdzPathwaysGEO.Rcheck/00check.log’
for details.



Installation output

KEGGdzPathwaysGEO.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL KEGGdzPathwaysGEO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘KEGGdzPathwaysGEO’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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
* DONE (KEGGdzPathwaysGEO)

Tests output


Example timings

KEGGdzPathwaysGEO.Rcheck/KEGGdzPathwaysGEO-Ex.timings

nameusersystemelapsed
GSE12970.0630.0000.063
GSE147620.1410.0040.144
GSE154710.3040.0160.320
GSE165150.1590.0080.167
GSE188420.3800.0080.388
GSE191880.6420.0330.674
GSE197280.1460.0070.155
GSE201530.1050.0070.113
GSE202910.1050.0000.105
GSE213540.1620.0160.179
GSE34670.120.000.12
GSE35850.0430.0000.043
GSE36780.110.000.11
GSE41070.1350.0090.143
GSE5281_EC0.1280.0000.127
GSE5281_HIP0.1410.0000.140
GSE5281_VCX0.1530.0070.160
GSE6956AA0.0390.0000.038
GSE6956C0.0830.0040.087
GSE7810.0460.0010.046
GSE86710.2650.0070.272
GSE87620.1290.0040.133
GSE93480.3320.0080.340
GSE94760.0990.0150.114
KEGGdzPathwaysGEO-package0.3250.0090.341