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CHECK report for KEGGdzPathwaysGEO on malbec2

This page was generated on 2020-10-15 20:45:48 -0400 (Thu, 15 Oct 2020).

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 192/391HostnameOS / ArchINSTALLBUILDCHECK
KEGGdzPathwaysGEO 1.26.0
Gaurav Bhatti
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO
Branch: RELEASE_3_11
Last Commit: f5f97cf
Last Changed Date: 2020-04-27 15:11:51 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: KEGGdzPathwaysGEO
Version: 1.26.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:KEGGdzPathwaysGEO.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings KEGGdzPathwaysGEO_1.26.0.tar.gz
StartedAt: 2020-10-15 13:34:50 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 13:40:14 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 324.4 seconds
RetCode: 0
Status:  OK 
CheckDir: KEGGdzPathwaysGEO.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:KEGGdzPathwaysGEO.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings KEGGdzPathwaysGEO_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/KEGGdzPathwaysGEO.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.26.0’
* 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 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-data-experiment/meat/KEGGdzPathwaysGEO.Rcheck/00check.log’
for details.



Installation output

KEGGdzPathwaysGEO.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL KEGGdzPathwaysGEO
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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
GSE12970.0460.0090.054
GSE147620.1280.0000.128
GSE154710.3090.0120.321
GSE165150.1750.0040.179
GSE188420.3660.0190.386
GSE191880.6230.0510.675
GSE197280.1240.0040.128
GSE201530.1040.0080.112
GSE202910.0690.0040.073
GSE213540.1150.0040.119
GSE34670.1140.0000.115
GSE35850.0390.0000.039
GSE36780.0960.0030.099
GSE41070.1300.0010.130
GSE5281_EC0.130.000.13
GSE5281_HIP0.1360.0000.135
GSE5281_VCX0.1520.0040.156
GSE6956AA0.0360.0000.036
GSE6956C0.0770.0040.081
GSE7810.0450.0000.045
GSE86710.2610.0080.269
GSE87620.1150.0150.131
GSE93480.3310.0080.338
GSE94760.1180.0010.119
KEGGdzPathwaysGEO-package0.3050.0070.330