Back to Build/check report for BioC 3.11 experimental data

CHECK report for GGdata on malbec2

This page was generated on 2020-10-15 20:45:47 -0400 (Thu, 15 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GGdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 142/391HostnameOS / ArchINSTALLBUILDCHECK
GGdata 1.26.0
VJ Carey
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/GGdata
Branch: RELEASE_3_11
Last Commit: d0a0f86
Last Changed Date: 2020-04-27 14:54:23 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: GGdata
Version: 1.26.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GGdata.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GGdata_1.26.0.tar.gz
StartedAt: 2020-10-15 13:25:30 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 13:27:59 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 149.2 seconds
RetCode: 0
Status:  OK 
CheckDir: GGdata.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GGdata.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GGdata_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/GGdata.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGdata/DESCRIPTION’ ... OK
* this is package ‘GGdata’ 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 ‘GGdata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 71.9Mb
  sub-directories of 1Mb or more:
    data   21.1Mb
    parts  50.8Mb
* checking package 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 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:
  ‘AnnotationDbi’ ‘GGBase’ ‘illuminaHumanv1.db’ ‘methods’ ‘snpStats’
  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 ‘GGdata/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste("To get a tailored smlSet, use getSS(\"",     pkgname, "\", [chrvec])", sep = ""), "\n")
    packageStartupMessage("available chromosomes are named ", paste(selectSome(cn),     collapse = ", "), "\n")

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
hmceuB36-pkg 12.747  0.344  16.648
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-data-experiment/meat/GGdata.Rcheck/00check.log’
for details.



Installation output

GGdata.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GGdata
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘GGdata’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (GGdata)

Tests output


Example timings

GGdata.Rcheck/GGdata-Ex.timings

nameusersystemelapsed
hmceuB36-pkg12.747 0.34416.648