Back to Build/check report for BioC 3.16 experimental data
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This page was generated on 2023-04-11 14:50:27 -0400 (Tue, 11 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
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 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 163/416HostnameOS / ArchINSTALLBUILDCHECK
harbChIP 1.36.0  (landing page)
VJ Carey
Snapshot Date: 2023-04-11 07:30:01 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/harbChIP
git_branch: RELEASE_3_16
git_last_commit: c711160
git_last_commit_date: 2022-11-01 10:39:44 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: harbChIP
Version: 1.36.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:harbChIP.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings harbChIP_1.36.0.tar.gz
StartedAt: 2023-04-11 11:50:34 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 11:51:47 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 72.5 seconds
RetCode: 0
Status:   OK  
CheckDir: harbChIP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:harbChIP.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings harbChIP_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/harbChIP.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘harbChIP/DESCRIPTION’ ... OK
* this is package ‘harbChIP’ version ‘1.36.0’
* 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 loading without being on the library search path ... 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 ...
  ‘yeastUpstream.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/harbChIP.Rcheck/00check.log’
for details.



Installation output

harbChIP.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL harbChIP
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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
allhex0.1760.0120.188
buildUpstreamSeqs2000
chkMotif4TF000
harbChIP0.7140.0520.766
sceUpstream0.1590.0000.158
upstreamSeqs-class0.1640.0000.163