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CHECK report for yeastExpData on malbec2

This page was generated on 2021-01-14 15:59:06 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE yeastExpData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 380/385HostnameOS / ArchINSTALLBUILDCHECK
yeastExpData 0.37.0
R. Gentleman
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/yeastExpData
Branch: master
Last Commit: f9103f1
Last Changed Date: 2020-10-27 09:47:15 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS 

Summary

Package: yeastExpData
Version: 0.37.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:yeastExpData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings yeastExpData_0.37.0.tar.gz
StartedAt: 2021-01-14 13:02:24 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 13:02:44 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 20.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: yeastExpData.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:yeastExpData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings yeastExpData_0.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/yeastExpData.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yeastExpData/DESCRIPTION’ ... OK
* this is package ‘yeastExpData’ version ‘0.37.0’
* 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 ‘yeastExpData’ 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 ... WARNING
Data codoc mismatches from documentation object 'gfp':
Variables in data frame 'gfp'
  Code: ER ER_to_Golgi GFP_tagged GFP_visualized Golgi TAP_visualized
        abundance actin ambiguous bud bud_neck cell_periphery cytoplasm
        early_Golgi endosome error gene_name late_Golgi lipid_particle
        localization_summary microtubule missingAbundance mitochondrion
        nuclear_periphery nucleolus nucleus orfid peroxisome
        punctate_composite spindle_pole vacuolar_membrane vacuole yORF
  Docs: GFP_tagged GFP_visualized TAP_visualized abundance error
        gene_name localization_summary orfid yORF

Data codoc mismatches from documentation object 'proteinProperties':
Variables in data frame 'proteinProperties'
  Code: ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER
        SGDID THR TRP TYR VAL aromaticity cai codonBias cterm fop gravy
        length molwt nterm pi type yORF
  Docs: SGDID cai codonBias cterm length molwt nterm pi yORF

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘lattice’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  Warning: large data file saved inefficiently:
                 size ASCII compress
  ccyclered.rda 364Kb FALSE     none
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                        old_size new_size compress
  ccyclered.rda            364Kb     59Kb       xz
  fcabundance.rda          110Kb     67Kb       xz
  gfp.rda                  118Kb     60Kb       xz
  litG.rda                  22Kb      8Kb       xz
  proteinProperties.rda    488Kb    311Kb       xz
  y2hG.rda                  22Kb      9Kb       xz
* 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: 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/yeastExpData.Rcheck/00check.log’
for details.



Installation output

yeastExpData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL yeastExpData
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘yeastExpData’ ...
** using staged installation
** data
** 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 (yeastExpData)

Tests output


Example timings

yeastExpData.Rcheck/yeastExpData-Ex.timings

nameusersystemelapsed
ccyclered0.0160.0040.020
fcabundance0.1810.0040.185
gfp0.2000.0160.215
litG0.0170.0000.017
nPdist0.0010.0000.001
proteinProperties0.3480.0000.348