Back to Build/check report for BioC 3.10 experimental data

CHECK report for NestLink on malbec1

This page was generated on 2020-04-14 17:46:30 -0400 (Tue, 14 Apr 2020).

Package 249/384HostnameOS / ArchINSTALLBUILDCHECK
NestLink 1.2.0
Christian Panse
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/NestLink
Branch: RELEASE_3_10
Last Commit: 403a32f
Last Changed Date: 2019-10-29 13:29:55 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: NestLink
Version: 1.2.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings NestLink_1.2.0.tar.gz
StartedAt: 2020-04-14 13:57:09 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 14:03:56 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 407.6 seconds
RetCode: 0
Status:  OK 
CheckDir: NestLink.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings NestLink_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/NestLink.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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 or elapsed time > 5s
                            user system elapsed
runNGSAnalysis           154.056  0.148 156.132
getExperimentHubFilename  17.684  0.232  19.757
getFC                      5.400  0.048   5.651
F255744                    4.864  0.172   5.500
* 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-3.10-data-experiment/meat/NestLink.Rcheck/00check.log’
for details.



Installation output

NestLink.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL NestLink
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
 21.940   0.672  23.569 

Example timings

NestLink.Rcheck/NestLink-Ex.timings

nameusersystemelapsed
F2557444.8640.1725.500
NB.unambiguous3.7120.0283.933
NB.unique3.9040.0124.160
PGexport2.3720.0322.783
WU1601184.3360.0444.607
compose_GPGx8cTerm0.0080.0000.008
compose_GPx10R0.0080.0000.006
compose_GSx7cTerm0.0040.0040.008
dot-ssrc.mascot4.4400.0444.676
getExperimentHubFilename17.684 0.23219.757
getFC5.4000.0485.651
getNB3.5280.0283.827
nanobodyFlycodeLinking.as.fasta2.2200.0282.460
nanobodyFlycodeLinking.summary2.6840.0282.901
plot_in_silico_LCMS_map1.5760.0041.581
runNGSAnalysis154.056 0.148156.132
twoPatternReadFilter0.0120.0000.013