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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 Oct 2021).

CHECK results for harbChIP on nebbiolo2

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

raw results

Package 161/404HostnameOS / ArchINSTALLBUILDCHECK
harbChIP 1.31.0  (landing page)
VJ Carey
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/harbChIP
git_branch: master
git_last_commit: a6e46a3
git_last_commit_date: 2021-05-19 11:25:08 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: harbChIP
Version: 1.31.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:harbChIP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings harbChIP_1.31.0.tar.gz
StartedAt: 2021-10-16 12:17:53 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 12:18:54 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 61.4 seconds
RetCode: 0
Status:   OK  
CheckDir: harbChIP.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:harbChIP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings harbChIP_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/harbChIP.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘harbChIP/DESCRIPTION’ ... OK
* this is package ‘harbChIP’ version ‘1.31.0’
* 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 ‘harbChIP’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘Biostrings’ ‘IRanges’ ‘tools’
  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
chkAllUS: no visible binding for global variable ‘sceUpstr’
chkAllUS : <anonymous>: no visible global function definition for
  ‘countPattern’
chkMotif4TF: no visible global function definition for ‘sampleNames’
chkMotif4TF: no visible global function definition for ‘exprs’
Nmers,numeric-character-upstreamSeqs: no visible global function
  definition for ‘Views’
Undefined global functions or variables:
  Views countPattern exprs sampleNames sceUpstr
* 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 ... 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/harbChIP.Rcheck/00check.log’
for details.



Installation output

harbChIP.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL harbChIP
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘harbChIP’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** 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 (harbChIP)

Tests output


Example timings

harbChIP.Rcheck/harbChIP-Ex.timings

nameusersystemelapsed
allhex0.1790.0160.196
buildUpstreamSeqs2000
chkMotif4TF000
harbChIP0.7410.0400.782
sceUpstream0.1760.0000.175
upstreamSeqs-class0.1740.0000.174