Back to Multiple platform build/check report for BioC 3.13 experimental data
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

CHECK report for davidTiling on malbec2

This page was generated on 2021-01-14 15:58:59 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE davidTiling PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 89/385HostnameOS / ArchINSTALLBUILDCHECK
davidTiling 1.31.0
Wolfgang Huber
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/davidTiling
Branch: master
Last Commit: 0c228f3
Last Changed Date: 2020-10-27 09:45:05 -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: davidTiling
Version: 1.31.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:davidTiling.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings davidTiling_1.31.0.tar.gz
StartedAt: 2021-01-14 11:57:54 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 12:02:21 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 266.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: davidTiling.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:davidTiling.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings davidTiling_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/davidTiling.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 ‘davidTiling/DESCRIPTION’ ... OK
* this is package ‘davidTiling’ 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 ‘davidTiling’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 538.1Mb
  sub-directories of 1Mb or more:
    celfiles  305.9Mb
    data      229.5Mb
    website     2.3Mb
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘GO.db’ ‘tilingArray’
  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
GOHyperG: no visible global function definition for ‘phyper’
GOHyperG: no visible binding for global variable ‘GOTERM’
GOHyperG: no visible global function definition for
  ‘replaceSystematicByCommonName’
GOHyperG: no visible global function definition for ‘Term’
GOHyperG: no visible global function definition for ‘abline’
colMedians: no visible binding for global variable ‘median’
getAllGO: no visible binding for global variable ‘GOMFANCESTOR’
getAllGO: no visible binding for global variable ‘GOBPANCESTOR’
getAllGO: no visible binding for global variable ‘GOCCANCESTOR’
movingWindow: no visible global function definition for ‘median’
movingWindow : <anonymous>: no visible global function definition for
  ‘median’
scatterWithHist: no visible global function definition for ‘hist’
scatterWithHist: no visible global function definition for ‘layout’
scatterWithHist: no visible global function definition for ‘par’
scatterWithHist: no visible global function definition for ‘barplot’
scatterWithHist: no visible global function definition for ‘text’
scoreSegments: no visible global function definition for ‘data’
scoreSegments: no visible binding for global variable ‘yeastFeatures’
scoreSegments: no visible binding for global variable ‘chrs’
scoreSegments: no visible global function definition for ‘otherStrand’
scoreSegments: no visible global function definition for ‘median’
scoreSegments: no visible global function definition for ‘posMin’
showDens: no visible global function definition for ‘hist’
showDens: no visible global function definition for ‘axis’
showDens: no visible global function definition for ‘polygon’
zscore: no visible global function definition for ‘sd’
Undefined global functions or variables:
  GOBPANCESTOR GOCCANCESTOR GOMFANCESTOR GOTERM Term abline axis
  barplot chrs data hist layout median otherStrand par phyper polygon
  posMin replaceSystematicByCommonName sd text yeastFeatures
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "hist", "layout",
             "par", "polygon", "text")
  importFrom("stats", "median", "phyper", "sd")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: GOHyperG.Rd:34-35: Dropping empty section \examples
prepare_Rd: getGO.Rd:32-33: Dropping empty section \examples
prepare_Rd: scatterWithHist.Rd:19-20: Dropping empty section \details
prepare_Rd: scoreSegments.Rd:103-104: Dropping empty section \examples
* 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 ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Archi_RT_positions.txt’, ‘strongConservedNovelIsolated.txt’,
    ‘utrmap-GOcategories.txt’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
davidTiling 27.446  0.495  27.942
probeAnno    5.348  0.240   5.588
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/davidTiling.Rcheck/00check.log’
for details.



Installation output

davidTiling.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL davidTiling
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘davidTiling’ ...
** using staged installation
** R
** data
** inst
** 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 (davidTiling)

Tests output


Example timings

davidTiling.Rcheck/davidTiling-Ex.timings

nameusersystemelapsed
davidTiling27.446 0.49527.942
getAttributeField0.0000.0000.001
gff0.4090.0160.425
probeAnno5.3480.2405.588
scatterWithHist0.0210.0000.021
showDens0.0050.0000.005
yeastFeatures0.0000.0030.002