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This page was generated on 2023-10-12 14:51:35 -0400 (Thu, 12 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
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

Package 264/421HostnameOS / ArchINSTALLBUILDCHECK
NestLink 1.16.0  (landing page)
Lennart Opitz
Snapshot Date: 2023-10-12 07:30:02 -0400 (Thu, 12 Oct 2023)
git_url: https://git.bioconductor.org/packages/NestLink
git_branch: RELEASE_3_17
git_last_commit: bd0e725
git_last_commit_date: 2023-04-25 10:46:37 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for NestLink on nebbiolo1


To the developers/maintainers of the NestLink package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: NestLink
Version: 1.16.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings NestLink_1.16.0.tar.gz
StartedAt: 2023-10-12 11:46:33 -0400 (Thu, 12 Oct 2023)
EndedAt: 2023-10-12 11:57:47 -0400 (Thu, 12 Oct 2023)
EllapsedTime: 673.7 seconds
RetCode: 0
Status:   OK  
CheckDir: NestLink.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings NestLink_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/NestLink.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘NestLink/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NestLink’ version ‘1.16.0’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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           138.316  1.102 139.753
getExperimentHubFilename  11.331  0.821  14.409
getFC                      4.591  0.181   5.041
* 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 ...
  ‘analyze-flycode-detectibilty.Rmd’ using ‘UTF-8’... OK
  ‘compare-predicted-observed-flycodes.Rmd’ using ‘UTF-8’... OK
  ‘link-nanobodies-flycodes.Rmd’ using ‘UTF-8’... OK
  ‘make-data.Rmd’ using ‘UTF-8’... OK
  ‘simulate-flycodes.Rmd’ using ‘UTF-8’... OK
  ‘supplement-note1.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-data-experiment/meat/NestLink.Rcheck/00check.log’
for details.



Installation output

NestLink.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NestLink
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 
 18.894   1.461  21.139 

Example timings

NestLink.Rcheck/NestLink-Ex.timings

nameusersystemelapsed
F2557441.8600.2242.500
NB.unambiguous2.7800.2373.289
NB.unique3.6060.3474.122
PGexport1.4010.1681.844
WU1601182.6010.2163.092
compose_GPGx8cTerm0.0070.0000.007
compose_GPx10R0.0040.0000.004
compose_GSx7cTerm0.0050.0030.008
dot-ssrc.mascot2.8300.2653.369
getExperimentHubFilename11.331 0.82114.409
getFC4.5910.1815.041
getNB2.7220.1043.093
nanobodyFlycodeLinking.as.fasta1.3490.0881.732
nanobodyFlycodeLinking.summary1.4390.0841.687
plot_in_silico_LCMS_map1.7500.0281.779
runNGSAnalysis138.316 1.102139.753
twoPatternReadFilter0.0170.0000.017