Back to Multiple platform build/check report for BioC 3.9 experimental data

CHECK report for NestLink on malbec2

This page was generated on 2019-10-17 16:51:39 -0400 (Thu, 17 Oct 2019).

Package 243/371HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NestLink 1.0.0
Christian Panse
Snapshot Date: 2019-10-17 09:00:12 -0400 (Thu, 17 Oct 2019)
URL: https://git.bioconductor.org/packages/NestLink
Branch: RELEASE_3_9
Last Commit: 4b44f10
Last Changed Date: 2019-05-02 11:56:53 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: NestLink
Version: 1.0.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings NestLink_1.0.0.tar.gz
StartedAt: 2019-10-17 13:34:57 -0400 (Thu, 17 Oct 2019)
EndedAt: 2019-10-17 13:41:20 -0400 (Thu, 17 Oct 2019)
EllapsedTime: 383.4 seconds
RetCode: 0
Status:  OK 
CheckDir: NestLink.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings NestLink_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/NestLink.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.0.0’
* 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 
* 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 or elapsed time > 5s
                            user system elapsed
runNGSAnalysis           146.122  0.172 147.750
getExperimentHubFilename  16.013  0.144  17.389
getFC                      5.148  0.024   5.302
F255744                    4.256  0.168   6.332
* 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-3.9-data-experiment/meat/NestLink.Rcheck/00check.log’
for details.



Installation output

NestLink.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL NestLink
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.407   0.661  21.886 

Example timings

NestLink.Rcheck/NestLink-Ex.timings

nameusersystemelapsed
F2557444.2560.1686.332
NB.unambiguous3.4190.0563.618
NB.unique3.1890.0163.341
PGexport1.8300.0242.009
WU1601183.7270.0524.950
compose_GPGx8cTerm0.0050.0020.007
compose_GPx10R0.0040.0000.005
compose_GSx7cTerm0.0070.0000.007
dot-ssrc.mascot2.7270.0162.874
getExperimentHubFilename16.013 0.14417.389
getFC5.1480.0245.302
getNB3.0140.0403.200
nanobodyFlycodeLinking.as.fasta1.7240.0122.112
nanobodyFlycodeLinking.summary1.7710.0241.930
plot_in_silico_LCMS_map1.4710.0081.478
runNGSAnalysis146.122 0.172147.750
twoPatternReadFilter0.0120.0000.012