Back to Build/check report for BioC 3.11 experimental data

CHECK report for MSstatsBioData on malbec2

This page was generated on 2020-10-15 20:45:52 -0400 (Thu, 15 Oct 2020).

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 241/391HostnameOS / ArchINSTALLBUILDCHECK
MSstatsBioData 1.10.0
Meena Choi
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/MSstatsBioData
Branch: RELEASE_3_11
Last Commit: 11f0e4f
Last Changed Date: 2020-04-27 16:21:07 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: MSstatsBioData
Version: 1.10.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSstatsBioData.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSstatsBioData_1.10.0.tar.gz
StartedAt: 2020-10-15 13:46:07 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 13:49:02 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 174.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MSstatsBioData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSstatsBioData.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSstatsBioData_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-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 ‘1.10.0’
* 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 ... OK
* 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 ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* 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 65.652  0.028  66.689
DDA_cardio         31.010  0.358  40.256
SRM_crc_training   18.792  0.000  19.601
SRM_mpm_validation  7.993  0.004  10.138
SRM_mpm_training    7.485  0.008  10.925
SRM_yeast           4.852  0.016   5.462
SRM_ovarian         4.084  0.008   7.545
* 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-3.11-data-experiment/meat/MSstatsBioData.Rcheck/00check.log’
for details.



Installation output

MSstatsBioData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MSstatsBioData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-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_cardio31.010 0.35840.256
SRM_crc_training18.792 0.00019.601
SRM_crc_validation65.652 0.02866.689
SRM_mpm_training 7.485 0.00810.925
SRM_mpm_validation 7.993 0.00410.138
SRM_ovarian4.0840.0087.545
SRM_yeast4.8520.0165.462