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CHECK report for seq2pathway.data on malbec1

This page was generated on 2021-05-06 14:10:14 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the seq2pathway.data package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 336/398HostnameOS / ArchINSTALLBUILDCHECK
seq2pathway.data 1.22.0  (landing page)
Xinan Holly Yang
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/seq2pathway.data
Branch: RELEASE_3_12
Last Commit: 5ba32cf
Last Changed Date: 2020-10-27 10:11:18 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository

Summary

Package: seq2pathway.data
Version: 1.22.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:seq2pathway.data.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings seq2pathway.data_1.22.0.tar.gz
StartedAt: 2021-05-06 12:44:42 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 12:45:09 -0400 (Thu, 06 May 2021)
EllapsedTime: 26.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: seq2pathway.data.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:seq2pathway.data.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings seq2pathway.data_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/seq2pathway.data.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seq2pathway.data/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seq2pathway.data’ version ‘1.22.0’
* 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 ‘seq2pathway.data’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 225.9Mb
  sub-directories of 1Mb or more:
    data       4.3Mb
    extdata  221.4Mb
* 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 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 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 ... WARNING
File ‘data/datalist’ contains malformed line(s):
  ‘’ ‘’
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/seq2pathway.data.Rcheck/00check.log’
for details.



Installation output

seq2pathway.data.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL seq2pathway.data
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘seq2pathway.data’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** 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
* DONE (seq2pathway.data)

Tests output


Example timings

seq2pathway.data.Rcheck/seq2pathway.data-Ex.timings

nameusersystemelapsed
Des_BP_list0.0520.0000.052
Des_CC_list0.0200.0080.028
Des_MF_list0.0440.0120.054
GO_BP_list0.0760.0040.079
GO_CC_list0.1000.0640.164
GO_GENCODE_df_hg_v190.0240.0000.022
GO_GENCODE_df_hg_v200.0160.0000.019
GO_GENCODE_df_mm_vM10.0120.0000.015
GO_GENCODE_df_mm_vM30.0160.0000.016
GO_GENCODE_df_mm_vM40.0080.0000.009
GO_MF_list0.0480.0000.046
Msig_GENCODE_df_hg_v190.0240.0000.024
Msig_GENCODE_df_hg_v200.0240.0000.023
Msig_GENCODE_df_mm_vM10.0160.0000.017
Msig_GENCODE_df_mm_vM30.0160.0000.018
Msig_GENCODE_df_mm_vM40.0080.0040.010
gencode_coding0.2800.0000.281