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CHECK report for MSstatsBioData on nebbiolo1

This page was generated on 2021-01-14 14:10:34 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE MSstatsBioData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 246/398HostnameOS / ArchINSTALLBUILDCHECK
MSstatsBioData 1.12.0
Meena Choi
Snapshot Date: 2021-01-14 09:00:17 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/MSstatsBioData
Branch: RELEASE_3_12
Last Commit: e2631a8
Last Changed Date: 2020-10-27 10:23:13 -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: MSstatsBioData
Version: 1.12.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MSstatsBioData.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MSstatsBioData_1.12.0.tar.gz
StartedAt: 2021-01-14 11:07:21 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:09:26 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 124.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MSstatsBioData.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:MSstatsBioData.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MSstatsBioData_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/MSstatsBioData.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 ‘MSstatsBioData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsBioData’ version ‘1.12.0’
* package encoding: UTF-8
* 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 ‘MSstatsBioData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... WARNING
File ‘data/datalist’ contains malformed line(s):
  ‘’
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
SRM_crc_validation 46.924  0.286  47.214
DDA_cardio         24.246  0.506  24.764
SRM_crc_training   13.518  0.504  14.024
SRM_mpm_validation  5.612  0.008   5.621
SRM_mpm_training    5.002  0.025   5.027
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/MSstatsBioData.Rcheck/00check.log’
for details.



Installation output

MSstatsBioData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MSstatsBioData
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘MSstatsBioData’ ...
** using staged installation
** data
*** moving datasets to lazyload DB
** inst
** 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 (MSstatsBioData)

Tests output


Example timings

MSstatsBioData.Rcheck/MSstatsBioData-Ex.timings

nameusersystemelapsed
DDA_cardio24.246 0.50624.764
SRM_crc_training13.518 0.50414.024
SRM_crc_validation46.924 0.28647.214
SRM_mpm_training5.0020.0255.027
SRM_mpm_validation5.6120.0085.621
SRM_ovarian2.4250.0122.437
SRM_yeast3.0690.0083.076