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CHECK report for hmyriB36 on malbec1

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

To the developers/maintainers of the hmyriB36 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 183/398HostnameOS / ArchINSTALLBUILDCHECK
hmyriB36 1.26.0  (landing page)
Vincent Carey
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/hmyriB36
Branch: RELEASE_3_12
Last Commit: 6a9b11e
Last Changed Date: 2020-10-27 09:50:57 -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: hmyriB36
Version: 1.26.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:hmyriB36.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings hmyriB36_1.26.0.tar.gz
StartedAt: 2021-05-06 12:13:57 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 12:16:20 -0400 (Thu, 06 May 2021)
EllapsedTime: 143.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: hmyriB36.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:hmyriB36.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings hmyriB36_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/hmyriB36.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 ‘hmyriB36/DESCRIPTION’ ... OK
* this is package ‘hmyriB36’ 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 ‘hmyriB36’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GGBase' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-data-experiment/meat/hmyriB36.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 79.8Mb
  sub-directories of 1Mb or more:
    data   21.1Mb
    parts  58.7Mb
* checking package 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:
  ‘GGBase’ ‘methods’
  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
File ‘hmyriB36/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste("To get a tailored smlSet, use getSS(\"",     pkgname, "\", [chrvec])", sep = ""))
    packageStartupMessage(paste("available chromosomes are named ",     paste(selectSome(cn), collapse = ", ")))

See section ‘Good practice’ in '?.onAttach'.
* 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
hmyriB36-pkg 13.892  0.368  16.366
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/hmyriB36.Rcheck/00check.log’
for details.



Installation output

hmyriB36.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL hmyriB36
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘hmyriB36’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'GGBase' is deprecated and will be removed from Bioconductor
  version 3.13 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: Package 'GGBase' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'GGBase' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (hmyriB36)

Tests output


Example timings

hmyriB36.Rcheck/hmyriB36-Ex.timings

nameusersystemelapsed
hmyriB36-pkg13.892 0.36816.366