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CHECK report for agilp on malbec1

This page was generated on 2021-05-06 12:26:45 -0400 (Thu, 06 May 2021).

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 39/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
agilp 3.22.0  (landing page)
Benny Chain
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/agilp
Branch: RELEASE_3_12
Last Commit: 7d089d5
Last Changed Date: 2020-10-27 10:47:29 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: agilp
Version: 3.22.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:agilp.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings agilp_3.22.0.tar.gz
StartedAt: 2021-05-05 22:54:25 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 22:54:41 -0400 (Wed, 05 May 2021)
EllapsedTime: 15.8 seconds
RetCode: 0
Status:   OK  
CheckDir: agilp.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:agilp.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings agilp_3.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/agilp.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘3.22.0’
* 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 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/agilp.Rcheck/00check.log’
for details.



Installation output

agilp.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL agilp
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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
AALoess0.0880.0000.101
AAProcess0.0760.0040.099
Baseline0.0640.0000.072
Equaliser0.0760.0040.079
IDswop0.3800.0040.383
Loader0.0720.0040.077
filenamex0.0000.0000.001