Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
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 1288/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
miRNAmeConverter 1.32.0 (landing page) Stefan J. Haunsberger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the miRNAmeConverter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miRNAmeConverter.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: miRNAmeConverter |
Version: 1.32.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:miRNAmeConverter.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings miRNAmeConverter_1.32.0.tar.gz |
StartedAt: 2024-10-17 02:32:20 -0400 (Thu, 17 Oct 2024) |
EndedAt: 2024-10-17 02:34:00 -0400 (Thu, 17 Oct 2024) |
EllapsedTime: 100.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: miRNAmeConverter.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:miRNAmeConverter.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings miRNAmeConverter_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/miRNAmeConverter.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘miRNAmeConverter/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘miRNAmeConverter’ version ‘1.32.0’ * checking package namespace information ... NOTE Found export directive that requires package ‘methods’: ‘exportMethods’ Remove all such namespace directives (if obsolete) or ensure that the DESCRIPTION Depends or Imports field contains ‘methods’. * checking package dependencies ... NOTE Vignette dependency required without any vignettes:: ‘knitr’ * 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 ‘miRNAmeConverter’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. OK * 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 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 ... NOTE MiRNANameConverter,ANY: no visible global function definition for ‘new’ Undefined global functions or variables: new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) translateMiRNAName.Rd:24: Lost braces; missing escapes or markup? 24 | {1=only sequences, 2=miRNA name and sequence}} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘getMirnasForMirbaseVersion’ Undocumented S4 methods: generic 'getMirnasForMirbaseVersion' and siglist 'MiRNANameConverter' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/miRNAmeConverter.Rcheck/00check.log’ for details.
miRNAmeConverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL miRNAmeConverter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘miRNAmeConverter’ ... ** using staged installation Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]], : It is recommended to use ‘given’ instead of ‘middle’. ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘MiRNANameConverter’ in package ‘miRNAmeConverter’ ** help *** installing help indices ** building package indices ** 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 (miRNAmeConverter)
miRNAmeConverter.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > library(testthat) > library(miRNAmeConverter) Loading required package: miRBaseVersions.db > > test_check("miRNAmeConverter") miRNA 'hsa-let-7a-3p' is the same as 'hsa-let-7a*'. ->hsa-let-7a-3p is the most recent one and will be used. The other ones will be neglected. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ] > > proc.time() user system elapsed 6.876 0.322 7.187
miRNAmeConverter.Rcheck/miRNAmeConverter-Ex.timings
name | user | system | elapsed | |
MiRNANameConverter-ANY-method | 0.112 | 0.052 | 0.237 | |
assessVersion | 0.219 | 0.000 | 0.220 | |
checkMiRNAName | 0.143 | 0.000 | 0.143 | |
currentVersion | 0.081 | 0.000 | 0.081 | |
miRNAmeConverter | 0.549 | 0.004 | 0.552 | |
nOrganisms | 0.08 | 0.00 | 0.08 | |
nTotalEntries | 0.085 | 0.000 | 0.084 | |
saveResults | 0.718 | 0.016 | 0.734 | |
translateMiRNAName | 0.730 | 0.000 | 0.729 | |
validOrganisms | 0.082 | 0.000 | 0.082 | |
validVersions | 0.091 | 0.000 | 0.091 | |