Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the APAlyzer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/APAlyzer.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 68/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
APAlyzer 1.13.0 (landing page) Ruijia Wang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | TIMEOUT | |||||||||
Package: APAlyzer |
Version: 1.13.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings APAlyzer_1.13.0.tar.gz |
StartedAt: 2023-02-27 20:31:34 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 21:11:35 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 2400.1 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: APAlyzer.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings APAlyzer_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/APAlyzer.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘APAlyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘APAlyzer’ version ‘1.13.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘APAlyzer’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... WARNING 'library' or 'require' call not declared from: ‘HybridMTest’ 'library' or 'require' call to ‘HybridMTest’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .GTF2LE: no visible binding for global variable ‘group_name’ .GTF2refUTRraw: no visible binding for global variable ‘GENEID’ .annotatePASRegion: no visible global function definition for ‘queryHits’ APABox: no visible binding for global variable ‘APAreg’ APABox: no visible binding for global variable ‘RED’ APAVolcano: no visible binding for global variable ‘APAreg’ APAVolcano: no visible binding for global variable ‘color’ PASEXP_IPA: no visible global function definition for ‘Print’ ThreeMostPairBam: no visible global function definition for ‘Print’ download_testbam: no visible global function definition for ‘download.file’ Undefined global functions or variables: APAreg GENEID Print RED color download.file group_name queryHits Consider adding importFrom("utils", "download.file") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: download_testbam.Rd:7-8: Dropping empty section \arguments * 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 ...
APAlyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL APAlyzer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘APAlyzer’ ... ** using staged installation ** R ** 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 (APAlyzer)
APAlyzer.Rcheck/APAlyzer-Ex.timings
name | user | system | elapsed | |
APABox | 0.511 | 0.024 | 0.536 | |
APAVolcano | 0.477 | 0.024 | 0.501 | |
APAdiff | 1.056 | 0.020 | 1.077 | |
GENEXP_CDS | 15.922 | 2.714 | 18.282 | |
PAS2GEF | 0.020 | 0.175 | 45.811 | |
PASEXP_3UTR | 17.422 | 4.027 | 24.560 | |
PASEXP_IPA | 16.531 | 1.552 | 19.145 | |
REF3UTR | 0.147 | 0.020 | 0.647 | |
REF4PAS | 0.159 | 0.008 | 0.635 | |
REFCDS | 0.670 | 0.028 | 0.698 | |
ThreeMostPairBam | 1.480 | 0.044 | 1.523 | |