Back to Build/check report for BioC 3.14 experimental data
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This page was generated on 2022-04-13 14:50:25 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for seq2pathway.data on nebbiolo2


To the developers/maintainers of the seq2pathway.data package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 342/408HostnameOS / ArchINSTALLBUILDCHECK
seq2pathway.data 1.26.0  (landing page)
Arjun Kinstlick
Snapshot Date: 2022-04-13 07:30:01 -0400 (Wed, 13 Apr 2022)
git_url: https://git.bioconductor.org/packages/seq2pathway.data
git_branch: RELEASE_3_14
git_last_commit: ee7800a
git_last_commit_date: 2021-10-26 12:12:17 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: seq2pathway.data
Version: 1.26.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:seq2pathway.data.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings seq2pathway.data_1.26.0.tar.gz
StartedAt: 2022-04-13 11:48:12 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 11:48:41 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 29.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: seq2pathway.data.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:seq2pathway.data.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings seq2pathway.data_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/seq2pathway.data.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.26.0’
* 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 ‘seq2pathway.data’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 227.3Mb
  sub-directories of 1Mb or more:
    data       5.7Mb
    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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 ... WARNING
Undocumented data sets:
  ‘GO_GENECODE_df_hg_v36’ ‘GO_GENECODE_df_mm_vM25’
  ‘Msig_GENECODE_df_hg_v36’ ‘Msig_GENECODE_df_mm_vM25’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-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-3.14-bioc/R/bin/R CMD INSTALL seq2pathway.data
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-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_list0.0310.0000.032
Des_CC_list0.0060.0000.005
Des_MF_list0.0090.0000.010
GO_BP_list0.0710.0000.071
GO_CC_list0.0400.0000.039
GO_GENCODE_df_hg_v190.0150.0000.015
GO_GENCODE_df_mm_vM10.0100.0000.011
GO_GENECODE_df_hg_v360.0080.0000.008
GO_GENECODE_df_mm_vM250.0090.0000.008
GO_MF_list0.0350.0000.034
Msig_GENCODE_df_hg_v190.0170.0000.017
Msig_GENCODE_df_mm_vM10.0120.0000.012
Msig_GENECODE_df_hg_v360.0140.0040.018
Msig_GENECODE_df_mm_vM250.0150.0000.015
gencode_coding0.1530.0000.153