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This page was generated on 2022-04-13 14:50:24 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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 255/408HostnameOS / ArchINSTALLBUILDCHECK
NestLink 1.10.0  (landing page)
Lennart Opitz
Snapshot Date: 2022-04-13 07:30:01 -0400 (Wed, 13 Apr 2022)
git_url: https://git.bioconductor.org/packages/NestLink
git_branch: RELEASE_3_14
git_last_commit: 3661e4f
git_last_commit_date: 2021-10-26 12:34:59 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NestLink
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2022-04-13 11:38:11 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 11:44:15 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 364.7 seconds
RetCode: 0
Status:   OK  
CheckDir: NestLink.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/NestLink.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.10.0’
* 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           107.914  0.972 109.454
getExperimentHubFilename  23.794  1.453  28.182
getFC                      5.574  0.300   6.231
WU160118                   4.583  0.372   5.423
F255744                    4.422  0.412   5.375
* 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

##############################################################################
##############################################################################
###
### 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
 22.545   1.520  25.325 

Example timings

NestLink.Rcheck/NestLink-Ex.timings

nameusersystemelapsed
F2557444.4220.4125.375
NB.unambiguous4.0430.2964.732
NB.unique4.0490.2484.654
PGexport3.0580.2603.684
WU1601184.5830.3725.423
compose_GPGx8cTerm0.0050.0000.006
compose_GPx10R0.0030.0000.003
compose_GSx7cTerm0.0060.0000.005
dot-ssrc.mascot3.6390.1724.103
getExperimentHubFilename23.794 1.45328.182
getFC5.5740.3006.231
getNB4.1700.1874.628
nanobodyFlycodeLinking.as.fasta3.0880.1803.780
nanobodyFlycodeLinking.summary3.2540.1423.767
plot_in_silico_LCMS_map1.2940.0181.313
runNGSAnalysis107.914 0.972109.454
twoPatternReadFilter0.0070.0040.012