Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 950/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
hiAnnotator 1.40.0 (landing page) Nirav V Malani
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the hiAnnotator package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hiAnnotator.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: hiAnnotator |
Version: 1.40.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hiAnnotator_1.40.0.tar.gz |
StartedAt: 2024-11-20 08:44:53 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 08:51:46 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 413.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hiAnnotator.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings hiAnnotator_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/hiAnnotator.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 ‘hiAnnotator/DESCRIPTION’ ... OK * this is package ‘hiAnnotator’ version ‘1.40.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘hiAnnotator’ 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 ... 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 get2NearestFeature: no visible global function definition for ‘IRanges’ get2NearestFeature: no visible global function definition for ‘mid’ get2NearestFeature: no visible binding for global variable ‘qStrand’ get2NearestFeature: no visible binding for global variable ‘subjectHits’ get2NearestFeature : <anonymous>: no visible binding for global variable ‘queryHits’ get2NearestFeature : <anonymous>: no visible binding for global variable ‘featureName’ getFeatureCounts : <anonymous>: no visible global function definition for ‘countQueryHits’ getFeatureCountsBig: no visible global function definition for ‘mid’ getLowestDists: no visible binding for global variable ‘queryHits’ getNearestFeature: no visible global function definition for ‘IRanges’ getNearestFeature: no visible global function definition for ‘mid’ getNearestFeature: no visible binding for global variable ‘queryHits’ getNearestFeature: no visible binding for global variable ‘n’ getNearestFeature: no visible binding for global variable ‘featureName’ getSitesInFeature: no visible global function definition for ‘overlapsAny’ getSitesInFeature: no visible binding for global variable ‘queryHits’ getSitesInFeature: no visible global function definition for ‘n’ getSitesInFeature: no visible binding for global variable ‘featureName’ makeChunks: no visible global function definition for ‘breakInChunks’ makeChunks: no visible global function definition for ‘detectCores’ makeChunks : <anonymous>: no visible global function definition for ‘keepSeqlevels’ makeChunks : <anonymous>: no visible global function definition for ‘seqlevelsInUse’ makeGRanges: no visible global function definition for ‘IRanges’ makeGRanges: no visible global function definition for ‘seqlengths’ makeGRanges: no visible global function definition for ‘seqlevels<-’ makeGRanges: no visible global function definition for ‘sortSeqlevels’ makeGRanges: no visible global function definition for ‘seqlevelsInUse’ makeGRanges: no visible global function definition for ‘seqlengths<-’ makeGRanges: no visible global function definition for ‘seqlevels’ Undefined global functions or variables: IRanges breakInChunks countQueryHits detectCores featureName keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels subjectHits * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/hiAnnotator.Rcheck/00check.log’ for details.
hiAnnotator.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL hiAnnotator ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘hiAnnotator’ ... ** using staged installation ** R ** data ** 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 (hiAnnotator)
hiAnnotator.Rcheck/hiAnnotator-Ex.timings
name | user | system | elapsed | |
cleanColname | 0.001 | 0.000 | 0.001 | |
doAnnotation | 1.074 | 0.020 | 1.096 | |
get2NearestFeature | 2.445 | 0.068 | 2.519 | |
getFeatureCounts | 0.606 | 0.004 | 0.612 | |
getFeatureCountsBig | 0.637 | 0.024 | 0.663 | |
getLowestDists | 0.111 | 0.000 | 0.112 | |
getNearestFeature | 1.385 | 0.004 | 1.393 | |
getRelevantCol | 0.006 | 0.000 | 0.005 | |
getSitesInFeature | 0.660 | 0.000 | 0.662 | |
getUCSCtable | 0 | 0 | 0 | |
getWindowLabel | 0.001 | 0.000 | 0.000 | |
makeChunks | 0.390 | 0.004 | 0.394 | |
makeGRanges | 0.347 | 0.008 | 0.355 | |
makeUCSCsession | 0 | 0 | 0 | |
plotdisFeature | 1.640 | 0.004 | 1.648 | |