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BioC experimental data: CHECK report for yriMulti on malbec2

This page was generated on 2017-10-18 15:09:46 -0400 (Wed, 18 Oct 2017).

Package 313/314HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
yriMulti 0.6.0
VJ Carey
Snapshot Date: 2017-10-18 09:00:07 -0400 (Wed, 18 Oct 2017)
URL: https://git.bioconductor.org/packages/yriMulti
Branch: RELEASE_3_5
Last Commit: 3e3183f
Last Changed Date: 2017-08-16 15:03:46 -0400 (Wed, 16 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: yriMulti
Version: 0.6.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings yriMulti_0.6.0.tar.gz
StartedAt: 2017-10-18 11:17:28 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 11:27:02 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 574.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: yriMulti.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings yriMulti_0.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/yriMulti.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 ‘yriMulti/DESCRIPTION’ ... OK
* this is package ‘yriMulti’ version ‘0.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘gQTLBase’ ‘SummarizedExperiment’ ‘GenomicRanges’ ‘Homo.sapiens’
  ‘dsQTL’ ‘geuvPack’ ‘MultiAssayExperiment’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘yriMulti’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 179.5Mb
  sub-directories of 1Mb or more:
    data  179.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘MultiAssayExperiment’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkGenomes: no visible global function definition for ‘genome’
mexGR: no visible global function definition for ‘subjectHits’
mexGR : embell: no visible global function definition for ‘DataFrame’
mexGR: no visible global function definition for ‘IRanges’
mexGR: no visible global function definition for ‘new’
plotEvM: no visible global function definition for ‘metadata’
pwplot: no visible global function definition for ‘experiments’
show,mexGR: no visible global function definition for ‘selectSome’
Undefined global functions or variables:
  DataFrame IRanges experiments genome metadata new selectSome
  subjectHits
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: mexGR.Rd:34-36: Dropping empty section \details
prepare_Rd: mexGR.Rd:51-53: Dropping empty section \note
prepare_Rd: mexGR.Rd:48-50: Dropping empty section \author
prepare_Rd: mexGR.Rd:45-47: Dropping empty section \references
prepare_Rd: mexGR.Rd:57-59: Dropping empty section \seealso
prepare_Rd: pwplot.Rd:7-9: Dropping empty section \description
prepare_Rd: pwplot.Rd:40-42: Dropping empty section \details
checkRd: (5) pwplot.Rd:0-70: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘demoMAE’
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
  banovichSE.rda  172.2Mb  114.9Mb       xz
  demoMAE.rda       6.8Mb    5.9Mb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mexGR      12.304  0.176  12.492
banovichSE  6.112  0.060   6.174
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  ‘GenomeInfoDb’ ‘GenomicFiles’ ‘VariantAnnotation’ ‘bibtex’
  ‘doParallel’ ‘gQTLstats’ ‘knitcitations’
* 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, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-data-experiment/meat/yriMulti.Rcheck/00check.log’
for details.


yriMulti.Rcheck/00install.out:

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

yriMulti.Rcheck/yriMulti-Ex.timings:

nameusersystemelapsed
banovichSE6.1120.0606.174
mexGR12.304 0.17612.492
pwplot0.2760.0040.280
yriMulti-package000