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CHECK report for ceu1kg on nebbiolo1

This page was generated on 2021-01-14 14:10:30 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE ceu1kg PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 52/398HostnameOS / ArchINSTALLBUILDCHECK
ceu1kg 0.28.0
VJ Carey
Snapshot Date: 2021-01-14 09:00:17 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/ceu1kg
Branch: RELEASE_3_12
Last Commit: baecf9f
Last Changed Date: 2020-10-27 09:52:08 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]

Summary

Package: ceu1kg
Version: 0.28.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ceu1kg.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ceu1kg_0.28.0.tar.gz
StartedAt: 2021-01-14 10:48:15 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 10:49:53 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 97.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ceu1kg.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:ceu1kg.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings ceu1kg_0.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/ceu1kg.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 ‘ceu1kg/DESCRIPTION’ ... OK
* this is package ‘ceu1kg’ version ‘0.28.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ceu1kg’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GGBase' is deprecated and will be removed from Bioconductor
  Warning: Package 'GGtools' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-data-experiment/meat/ceu1kg.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 80.9Mb
  sub-directories of 1Mb or more:
    data    11.1Mb
    extras   1.8Mb
    parts   67.9Mb
* 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 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 ... 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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/ceu1kg.Rcheck/00check.log’
for details.



Installation output

ceu1kg.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL ceu1kg
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘ceu1kg’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'GGBase' is deprecated and will be removed from Bioconductor
  version 3.13
Warning: Package 'GGtools' 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
Warning: Package 'GGtools' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (ceu1kg)

Tests output


Example timings

ceu1kg.Rcheck/ceu1kg-Ex.timings

nameusersystemelapsed
ceu1kg-package000