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CHECK report for XhybCasneuf on malbec2

This page was generated on 2021-01-21 16:01:23 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE XhybCasneuf PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 379/386HostnameOS / ArchINSTALLBUILDCHECK
XhybCasneuf 1.29.0
Tineke Casneuf
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/XhybCasneuf
Branch: master
Last Commit: e8fd05c
Last Changed Date: 2020-10-27 09:48:27 -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: XhybCasneuf
Version: 1.29.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:XhybCasneuf.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings XhybCasneuf_1.29.0.tar.gz
StartedAt: 2021-01-21 12:58:43 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 12:59:51 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 67.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: XhybCasneuf.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:XhybCasneuf.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings XhybCasneuf_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/XhybCasneuf.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 ‘XhybCasneuf/DESCRIPTION’ ... OK
* this is package ‘XhybCasneuf’ version ‘1.29.0’
* 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 ‘XhybCasneuf’ can be installed ... OK
* checking installed package size ... OK
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘affy’ ‘ath1121501cdf’ ‘grid’ ‘methods’ ‘tinesath1cdf’
  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
runSimulation : ourmedianpolish: no visible global function definition
  for ‘medpolish’
runSimulation: no visible global function definition for ‘hsv’
runSimulation: no visible global function definition for ‘rnorm’
runSimulation: no visible global function definition for ‘layout’
runSimulation: no visible global function definition for ‘par’
runSimulation: no visible global function definition for ‘matplot’
runSimulation: no visible binding for global variable
  ‘generateExprVal.method.mas’
runSimulation: no visible binding for global variable
  ‘generateExprVal.method.liwong’
runSimulation: no visible global function definition for ‘legend’
runSimulation: no visible global function definition for ‘cor’
plotExample,XhybExamples: no visible global function definition for
  ‘par’
plotExample,XhybExamples: no visible global function definition for
  ‘brewer.pal’
plotExample,XhybExamples: no visible global function definition for
  ‘matplot’
plotExample,XhybExamples: no visible global function definition for
  ‘lines’
plotExample,XhybExamples: no visible global function definition for
  ‘legend’
plotExample,XhybExamples : <anonymous>: no visible global function
  definition for ‘cor’
plotExample,XhybExamples: no visible global function definition for
  ‘abline’
Undefined global functions or variables:
  abline brewer.pal cor generateExprVal.method.liwong
  generateExprVal.method.mas hsv layout legend lines matplot medpolish
  par rnorm
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "matplot", "par")
  importFrom("stats", "cor", "medpolish", "rnorm")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... 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
  AffysTissue.noBl.rda      202Kb    154Kb       xz
  AffysTissue.rda           741Kb    491Kb       xz
  AffysTissueMC.rda         886Kb    589Kb       xz
  CustomsTissue.noBl.rda    153Kb    120Kb       xz
  CustomsTissue.rda         552Kb    373Kb       xz
  CustomsTissueMC.rda       688Kb    468Kb       xz
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/XhybCasneuf.Rcheck/00check.log’
for details.



Installation output

XhybCasneuf.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL XhybCasneuf
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘XhybCasneuf’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning messages:
1: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ath1121501cdf’ 
2: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘ath1121501cdf’ 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ath1121501cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘ath1121501cdf’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ath1121501cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘ath1121501cdf’
** testing if installed package keeps a record of temporary installation path
* DONE (XhybCasneuf)

Tests output


Example timings

XhybCasneuf.Rcheck/XhybCasneuf-Ex.timings

nameusersystemelapsed
AffysTissue0.1970.0160.213
CustomsTissue0.1030.0000.103
XhybExamples-class0.0650.0040.069
ex10.0210.0000.022
runSimulation0.0300.0000.031