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CHECK report for agilp on merida1

This page was generated on 2020-08-07 12:27:18 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE agilp PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 37/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
agilp 3.21.0
Benny Chain
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/agilp
Branch: master
Last Commit: 653f88f
Last Changed Date: 2020-04-27 14:31:27 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: agilp
Version: 3.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:agilp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings agilp_3.21.0.tar.gz
StartedAt: 2020-08-06 23:51:16 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 23:51:55 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 39.8 seconds
RetCode: 0
Status:  OK 
CheckDir: agilp.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:agilp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings agilp_3.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/agilp.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘agilp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘agilp’ version ‘3.21.0’
* 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 ‘agilp’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AALoess: no visible global function definition for ‘read.table’
AALoess: no visible global function definition for ‘loess’
AALoess: no visible global function definition for ‘predict’
AALoess: no visible global function definition for ‘write.table’
AALoess: no visible global function definition for ‘hist’
AAProcess: no visible global function definition for ‘read.table’
AAProcess: no visible global function definition for ‘write.table’
Baseline: no visible global function definition for ‘read.table’
Baseline: no visible global function definition for ‘write.table’
Equaliser: no visible global function definition for ‘read.table’
Equaliser: no visible global function definition for ‘write.table’
IDswop: no visible global function definition for ‘read.table’
IDswop: no visible binding for global variable ‘sd’
IDswop: no visible global function definition for ‘write.table’
Loader: no visible global function definition for ‘read.table’
Loader: no visible global function definition for ‘write.table’
filenamex: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  hist loess predict read.table sd write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "loess", "predict", "sd")
  importFrom("utils", "read.table", "write.table")
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 sizes of PDF files under ‘inst/doc’ ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/agilp.Rcheck/00check.log’
for details.



Installation output

agilp.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL agilp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘agilp’ ...
** using staged installation
** R
** 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 (agilp)

Tests output


Example timings

agilp.Rcheck/agilp-Ex.timings

nameusersystemelapsed
AALoess0.1200.0190.217
AAProcess0.0980.0090.183
Baseline0.0700.0050.122
Equaliser0.0810.0060.147
IDswop0.5580.0170.961
Loader0.1670.0630.389
filenamex0.0030.0010.004