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CHECK report for a4Preproc on nebbiolo1

This page was generated on 2020-10-18 12:27:32 -0400 (Sun, 18 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE a4Preproc PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 5/1874HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Preproc 1.37.0
Tobias Verbeke
Snapshot Date: 2020-10-17 14:41:49 -0400 (Sat, 17 Oct 2020)
URL: https://git.bioconductor.org/packages/a4Preproc
Branch: master
Last Commit: 950b2a6
Last Changed Date: 2020-04-27 14:25:20 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: a4Preproc
Version: 1.37.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:a4Preproc.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings a4Preproc_1.37.0.tar.gz
StartedAt: 2020-10-17 19:41:12 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 19:42:17 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 65.1 seconds
RetCode: 0
Status:  OK 
CheckDir: a4Preproc.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:a4Preproc.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings a4Preproc_1.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/a4Preproc.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Preproc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Preproc’ version ‘1.37.0’
* 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 ‘a4Preproc’ can be installed ... OK
* checking installed package size ... OK
* checking package 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
Package in Depends field not imported from: ‘methods’
  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
addGeneInfo: no visible global function definition for ‘annotation’
addGeneInfo: no visible global function definition for ‘featureNames’
addGeneInfo: no visible global function definition for ‘featureData’
addGeneInfo: no visible global function definition for ‘pData’
addGeneInfo: no visible global function definition for ‘pData<-’
addGeneInfo: no visible global function definition for ‘featureData<-’
addGeneInfo: no visible global function definition for ‘fvarMetadata’
addGeneInfo: no visible global function definition for ‘fvarMetadata<-’
Undefined global functions or variables:
  annotation featureData featureData<- featureNames fvarMetadata
  fvarMetadata<- pData pData<-
* 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 examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/a4Preproc.Rcheck/00check.log’
for details.



Installation output

a4Preproc.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL a4Preproc
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘a4Preproc’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (a4Preproc)

Tests output


Example timings

a4Preproc.Rcheck/a4Preproc-Ex.timings

nameusersystemelapsed
addGeneInfo2.2120.0762.288