BioC experimental data: CHECK report for HSMMSingleCell on malbec2

Package: HSMMSingleCell

Version: 0.110.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings HSMMSingleCell_0.110.0.tar.gz

StartedAt: 2017-10-18 10:51:46 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 10:53:00 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 73.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: HSMMSingleCell.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings HSMMSingleCell_0.110.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/HSMMSingleCell.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘0.110.0’
* 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 ... OK
* 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’
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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-data-experiment/meat/HSMMSingleCell.Rcheck/00check.log’
for details.

* installing *source* package ‘HSMMSingleCell’ ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HSMMSingleCell)