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CHECK report for HSMMSingleCell on malbec2

This page was generated on 2021-01-21 16:01:12 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE HSMMSingleCell PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 180/386HostnameOS / ArchINSTALLBUILDCHECK
HSMMSingleCell 1.11.0
Cole Trapnell
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/HSMMSingleCell
Branch: master
Last Commit: 58c28c0
Last Changed Date: 2020-10-27 10:09:00 -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: HSMMSingleCell
Version: 1.11.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HSMMSingleCell.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HSMMSingleCell_1.11.0.tar.gz
StartedAt: 2021-01-21 12:15:27 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 12:16:40 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 72.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: HSMMSingleCell.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:HSMMSingleCell.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings HSMMSingleCell_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/HSMMSingleCell.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 ‘HSMMSingleCell/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HSMMSingleCell’ version ‘1.11.0’
* 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 ‘HSMMSingleCell’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data  16.0Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘HSMM_expr_matrix’ ‘HSMM_sample_sheet’ ‘HSMM_gene_annotation’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                           old_size new_size compress
  HSMM_expr_matrix.rda       15.6Mb    9.0Mb       xz
  HSMM_gene_annotation.rda    451Kb    286Kb       xz
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘HSMMSingleCell-vignette-concordance.tex’,
    ‘HSMMSingleCell-vignette.Rnw’, ‘HSMMSingleCell-vignette.bbl’,
    ‘HSMMSingleCell-vignette.log’, ‘HSMMSingleCell-vignette.pdf’,
    ‘HSMMSingleCell-vignette.synctex.gz’,
    ‘HSMMSingleCell-vignette.tex’, ‘HSMMSingleCell-vignette.toc’,
    ‘monocle_alg.bib’, ‘whbiocvignette.sty’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/HSMMSingleCell-vignette.Rnw’
(Is a VignetteBuilder field missing?)
The following files look like leftovers/mistakes:
  ‘HSMMSingleCell-vignette.bbl’, ‘HSMMSingleCell-vignette.log’,
  ‘HSMMSingleCell-vignette.toc’
Please remove them from your package.
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/HSMMSingleCell.Rcheck/00check.log’
for details.



Installation output

HSMMSingleCell.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL HSMMSingleCell
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘HSMMSingleCell’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** 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 (HSMMSingleCell)

Tests output


Example timings