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) |
| Back to Build/check report for BioC 3.10 experimental data |
This page was generated on 2020-04-14 17:46:30 -0400 (Tue, 14 Apr 2020).
| Package 249/384 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| NestLink 1.2.0 Christian Panse
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| 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 |
##############################################################################
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### 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
###
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* 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.
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)
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
NestLink.Rcheck/NestLink-Ex.timings
| name | user | system | elapsed | |
| F255744 | 4.864 | 0.172 | 5.500 | |
| NB.unambiguous | 3.712 | 0.028 | 3.933 | |
| NB.unique | 3.904 | 0.012 | 4.160 | |
| PGexport | 2.372 | 0.032 | 2.783 | |
| WU160118 | 4.336 | 0.044 | 4.607 | |
| compose_GPGx8cTerm | 0.008 | 0.000 | 0.008 | |
| compose_GPx10R | 0.008 | 0.000 | 0.006 | |
| compose_GSx7cTerm | 0.004 | 0.004 | 0.008 | |
| dot-ssrc.mascot | 4.440 | 0.044 | 4.676 | |
| getExperimentHubFilename | 17.684 | 0.232 | 19.757 | |
| getFC | 5.400 | 0.048 | 5.651 | |
| getNB | 3.528 | 0.028 | 3.827 | |
| nanobodyFlycodeLinking.as.fasta | 2.220 | 0.028 | 2.460 | |
| nanobodyFlycodeLinking.summary | 2.684 | 0.028 | 2.901 | |
| plot_in_silico_LCMS_map | 1.576 | 0.004 | 1.581 | |
| runNGSAnalysis | 154.056 | 0.148 | 156.132 | |
| twoPatternReadFilter | 0.012 | 0.000 | 0.013 | |