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CHECK report for dyebiasexamples on malbec2

This page was generated on 2021-01-11 15:59:21 -0500 (Mon, 11 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE dyebiasexamples PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 107/385HostnameOS / ArchINSTALLBUILDCHECK
dyebiasexamples 1.31.0
Philip Lijnzaad
Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021)
URL: https://git.bioconductor.org/packages/dyebiasexamples
Branch: master
Last Commit: de2c585
Last Changed Date: 2020-10-27 09:51:10 -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: dyebiasexamples
Version: 1.31.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:dyebiasexamples.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings dyebiasexamples_1.31.0.tar.gz
StartedAt: 2021-01-11 11:59:02 -0500 (Mon, 11 Jan 2021)
EndedAt: 2021-01-11 11:59:57 -0500 (Mon, 11 Jan 2021)
EllapsedTime: 54.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: dyebiasexamples.Rcheck
Warnings: 5

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:dyebiasexamples.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings dyebiasexamples_1.31.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/dyebiasexamples.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 ‘dyebiasexamples/DESCRIPTION’ ... OK
* this is package ‘dyebiasexamples’ version ‘1.31.0’
* 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 ‘dyebiasexamples’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /home/biocbuild/bbs-3.13-data-experiment/meat/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
  Warning: /home/biocbuild/bbs-3.13-data-experiment/meat/dyebiasexamples/man/dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
See ‘/home/biocbuild/bbs-3.13-data-experiment/meat/dyebiasexamples.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 40.3Mb
  sub-directories of 1Mb or more:
    data        5.3Mb
    extradata  34.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘GEOquery’ ‘marray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.extract.measurements: no visible global function definition for
  ‘GSMList’
.extract.measurements : <anonymous>: no visible global function
  definition for ‘Table’
.extract.meta: no visible global function definition for ‘GSMList’
.extract.meta : <anonymous>: no visible global function definition for
  ‘Meta’
.gsmlist2targetinfo: no visible global function definition for
  ‘GSMList’
.gsmlist2targetinfo: no visible global function definition for ‘Meta’
.have.umcu.version: no visible global function definition for
  ‘package.version’
dyebias.geo2marray: no visible global function definition for ‘GSMList’
dyebias.geo2marray : <anonymous>: no visible global function definition
  for ‘Meta’
dyebias.geo2marray: no visible global function definition for ‘Meta’
dyebias.geo2marray: no visible global function definition for ‘GPLList’
dyebias.geo2marray: no visible global function definition for ‘Table’
dyebias.geo2marray: no visible global function definition for
  ‘read.marrayLayout’
dyebias.geo2marray: no visible global function definition for
  ‘Accession’
dyebias.geo2marray: no visible global function definition for
  ‘maControls<-’
dyebias.geo2marray: no visible global function definition for ‘new’
dyebias.geo2marray: no visible global function definition for
  ‘maLabels<-’
dyebias.geo2marray: no visible global function definition for
  ‘maInfo<-’
dyebias.geo2marray: no visible global function definition for ‘maRf’
dyebias.geo2marray: no visible global function definition for ‘maRb<-’
dyebias.geo2marray: no visible global function definition for ‘maGb<-’
dyebias.geo2marray: no visible global function definition for
  ‘maTargets<-’
dyebias.geo2marray: no visible global function definition for
  ‘maLayout<-’
dyebias.geo2marray: no visible global function definition for
  ‘maGnames<-’
Undefined global functions or variables:
  Accession GPLList GSMList Meta Table maControls<- maGb<- maGnames<-
  maInfo<- maLabels<- maLayout<- maRb<- maRf maTargets<- new
  package.version read.marrayLayout
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
prepare_Rd: dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
* 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
Files not of a type allowed in a ‘data’ directory:
  ‘README’
Please use e.g. ‘inst/extdata’ for non-R data files

* 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
  data.norm.rda    2.1Mb    1.5Mb       xz
  data.raw.rda     3.2Mb    2.2Mb       xz
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘ChangeLog’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/dyebiasexamples.Rcheck/00check.log’
for details.



Installation output

dyebiasexamples.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL dyebiasexamples
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘dyebiasexamples’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: /home/biocbuild/bbs-3.13-data-experiment/meat/dyebiasexamples/man/dyebias.geo2marray.Rd:10-17: Section \synopsis is unrecognized and will be dropped
Warning: /home/biocbuild/bbs-3.13-data-experiment/meat/dyebiasexamples/man/dyebias.umcu.proper.estimators.Rd:11-13: Section \synopsis is unrecognized and will be dropped
*** 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 (dyebiasexamples)

Tests output


Example timings

dyebiasexamples.Rcheck/dyebiasexamples-Ex.timings

nameusersystemelapsed
data.raw0.4240.0040.428
dyebias.geo2marray000
dyebias.umcu.proper.estimators0.9730.0121.000