Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:45 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 87/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
APAlyzer 1.19.0 (landing page) Ruijia Wang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the APAlyzer package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: APAlyzer |
Version: 1.19.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings APAlyzer_1.19.0.tar.gz |
StartedAt: 2024-08-21 02:29:43 -0000 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 02:57:53 -0000 (Wed, 21 Aug 2024) |
EllapsedTime: 1690.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: APAlyzer.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:APAlyzer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings APAlyzer_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/APAlyzer.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘APAlyzer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘APAlyzer’ version ‘1.19.0’ * 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 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 ... 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 ... ERROR Running examples in ‘APAlyzer-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: download_testbam > ### Title: download_testbam, download bam files of mouse testis and heart > ### Aliases: download_testbam > > ### ** Examples > > download_testbam() [1] "Download Heart_rep1" trying URL 'https://media.githubusercontent.com/media/RJWANGbioinfo/PAS_reference_RData_and_testing_data/master/bam/Heart_rep1.bam' Content type 'application/octet-stream' length 358373738 bytes (341.8 MB) ================================================== downloaded 341.8 MB [1] "Download Heart_rep2" trying URL 'https://media.githubusercontent.com/media/RJWANGbioinfo/PAS_reference_RData_and_testing_data/master/bam/Heart_rep2.bam' Content type 'application/octet-stream' length 341667659 bytes (325.8 MB) ================================================== downloaded 325.8 MB [1] "Download Heart_rep3" trying URL 'https://media.githubusercontent.com/media/RJWANGbioinfo/PAS_reference_RData_and_testing_data/master/bam/Heart_rep3.bam' Content type 'application/octet-stream' length 384305345 bytes (366.5 MB) ================= * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’/home/biocbuild/R/R-4.4.1/bin/BATCH: line 60: 2762028 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/runTests.R’ failed. Complete output: > require("APAlyzer") || stop("unable to load Package:APAlyzer") Loading required package: APAlyzer * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/APAlyzer.Rcheck/00check.log’ for details.
APAlyzer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL APAlyzer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-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/tests/runTests.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > require("APAlyzer") || stop("unable to load Package:APAlyzer") Loading required package: APAlyzer
APAlyzer.Rcheck/APAlyzer-Ex.timings
name | user | system | elapsed | |
APABox | 0.526 | 0.012 | 0.541 | |
APAVolcano | 0.528 | 0.012 | 0.541 | |
APAdiff | 2.304 | 0.020 | 2.329 | |
GENEXP_CDS | 15.035 | 2.183 | 16.909 | |
PAS2GEF | 0.050 | 0.144 | 79.723 | |
PASEXP_3UTR | 17.579 | 3.599 | 22.285 | |
PASEXP_IPA | 14.892 | 0.550 | 16.186 | |
REF3UTR | 0.213 | 0.005 | 0.277 | |
REF4PAS | 0.164 | 0.000 | 0.223 | |
REFCDS | 0.658 | 0.064 | 0.723 | |
ThreeMostPairBam | 2.636 | 0.603 | 3.245 | |