Back to Build/check report for BioC 3.19 experimental data |
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This page was generated on 2024-07-02 14:51 -0400 (Tue, 02 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
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 269/430 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
NestLink 1.20.0 (landing page) Lennart Opitz
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | |||||||
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. |
Package: NestLink |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NestLink_1.20.0.tar.gz |
StartedAt: 2024-07-02 11:47:27 -0400 (Tue, 02 Jul 2024) |
EndedAt: 2024-07-02 11:58:42 -0400 (Tue, 02 Jul 2024) |
EllapsedTime: 675.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NestLink.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:NestLink.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings NestLink_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/NestLink.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘NestLink/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘NestLink’ version ‘1.20.0’ * 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 code 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 whether 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 ... NOTE checkRd: (-1) runNGSAnalysis.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) runNGSAnalysis.Rd:35: Lost braces in \itemize; meant \describe ? * 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 130.150 1.044 131.525 getExperimentHubFilename 11.773 0.887 14.854 getFC 4.795 0.112 5.176 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-data-experiment/meat/NestLink.Rcheck/00check.log’ for details.
NestLink.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL NestLink ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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)
NestLink.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 20.012 1.188 22.087
NestLink.Rcheck/NestLink-Ex.timings
name | user | system | elapsed | |
F255744 | 2.595 | 0.195 | 3.192 | |
NB.unambiguous | 2.687 | 0.237 | 3.224 | |
NB.unique | 2.816 | 0.104 | 3.208 | |
PGexport | 1.443 | 0.124 | 1.835 | |
WU160118 | 3.617 | 0.203 | 4.090 | |
compose_GPGx8cTerm | 0.007 | 0.000 | 0.008 | |
compose_GPx10R | 0.001 | 0.003 | 0.005 | |
compose_GSx7cTerm | 0.004 | 0.004 | 0.008 | |
dot-ssrc.mascot | 3.060 | 0.133 | 3.459 | |
getExperimentHubFilename | 11.773 | 0.887 | 14.854 | |
getFC | 4.795 | 0.112 | 5.176 | |
getNB | 2.820 | 0.084 | 3.176 | |
nanobodyFlycodeLinking.as.fasta | 1.464 | 0.088 | 1.820 | |
nanobodyFlycodeLinking.summary | 1.471 | 0.141 | 1.913 | |
plot_in_silico_LCMS_map | 1.697 | 0.026 | 1.722 | |
runNGSAnalysis | 130.150 | 1.044 | 131.525 | |
twoPatternReadFilter | 0.017 | 0.000 | 0.017 | |