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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 Oct 2021).

CHECK results for NestLink on nebbiolo2

To the developers/maintainers of the NestLink package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 254/404HostnameOS / ArchINSTALLBUILDCHECK
NestLink 1.9.0  (landing page)
Lennart Opitz
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/NestLink
git_branch: master
git_last_commit: 861c35a
git_last_commit_date: 2021-05-19 12:07:22 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NestLink
Version: 1.9.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NestLink_1.9.0.tar.gz
StartedAt: 2021-10-16 12:26:16 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 12:32:25 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 368.6 seconds
RetCode: 0
Status:   OK  
CheckDir: NestLink.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NestLink_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/NestLink.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NestLink/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NestLink’ version ‘1.9.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'AnnotationHub', 'ExperimentHub', 'Biostrings', 'gplots', 'protViz',
  'ShortRead'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘NestLink’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Authors@R field gives persons with no role:
  Damien Morger <damien.morger@rqmicro.com>
* 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
runNGSAnalysis           117.889  0.893 119.437
getExperimentHubFilename  22.409  0.856  26.040
getFC                      5.429  0.099   5.847
F255744                    4.802  0.364   5.761
NB.unique                  4.358  0.284   5.031
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.14-data-experiment/meat/NestLink.Rcheck/00check.log’
for details.



Installation output

NestLink.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL NestLink
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘NestLink’ ...
** using staged installation
** R
** exec
** 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 (NestLink)

Tests output

NestLink.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #R
> 
> library(testthat)
> 
> suppressPackageStartupMessages(library(NestLink))
> 
> test_check("NestLink")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 10 ]
> 
> proc.time()
   user  system elapsed 
 23.103   1.531  25.965 

Example timings

NestLink.Rcheck/NestLink-Ex.timings

nameusersystemelapsed
F2557444.8020.3645.761
NB.unambiguous4.2040.3244.819
NB.unique4.3580.2845.031
PGexport3.5130.3764.310
WU1601183.7960.0834.170
compose_GPGx8cTerm0.0060.0000.006
compose_GPx10R0.0030.0000.004
compose_GSx7cTerm0.6770.0000.677
dot-ssrc.mascot3.5130.0413.931
getExperimentHubFilename22.409 0.85626.040
getFC5.4290.0995.847
getNB3.9680.0564.407
nanobodyFlycodeLinking.as.fasta2.8890.0653.374
nanobodyFlycodeLinking.summary2.7770.0473.126
plot_in_silico_LCMS_map1.4130.0121.426
runNGSAnalysis117.889 0.893119.437
twoPatternReadFilter0.0130.0000.012