Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-06 11:44 -0400 (Sat, 06 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
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 100/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ASpli 2.15.0 (landing page) Ariel Chernomoretz
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | NA | OK | ERROR | ||||||||||
To the developers/maintainers of the ASpli package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ASpli.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: ASpli |
Version: 2.15.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --no-vignettes --timings ASpli_2.15.0.tar.gz |
StartedAt: 2024-07-06 02:59:26 -0000 (Sat, 06 Jul 2024) |
EndedAt: 2024-07-06 03:21:32 -0000 (Sat, 06 Jul 2024) |
EllapsedTime: 1326.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ASpli.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --no-vignettes --timings ASpli_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ASpli.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 ‘ASpli/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ASpli’ version ‘2.15.0’ * 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 ‘ASpli’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/ASpli.Rcheck/00install.out’ for details. * 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 ... NOTE Namespace in Imports field not imported from: 'txdbmaker' All declared Imports should be used. * 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 ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘ASpli-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: jCounts > ### Title: Report PSI, PJU and PIR using experimental junctions > ### Aliases: jCounts AsDiscover > > ### ** Examples > > # Create a transcript DB from gff/gtf annotation file. > # Warnings in this examples can be ignored. > library(GenomicFeatures) Loading required package: GenomeInfoDb Loading required package: GenomicRanges > genomeTxDb <- txdbmaker::makeTxDbFromGFF( system.file('extdata','genes.mini.gtf', + package="ASpli") ) Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK > > # Create an ASpliFeatures object from TxDb > features <- binGenome( genomeTxDb ) * Number of extracted Genes = 10 * Number of extracted Exon Bins = 38 * Number of extracted intron bins = 34 * Number of extracted trascripts = 25 * Number of extracted junctions = 23 * Number of AS bins (not include external) = 17 * Number of AS bins (include external) = 17 * Classified as: ES bins = 1 (6%) IR bins = 3 (18%) Alt5'ss bins = 2 (12%) Alt3'ss bins = 2 (12%) Multiple AS bins = 9 (53%) classified as: ES bins = 1 (11%) IR bins = 4 (44%) Alt5'ss bins = 2 (22%) Alt3'ss bins = 1 (11%) Correcting Io ends, this might take a while... Genome binning completed > > # Define bam files, sample names and experimental factors for targets. > bamFileNames <- c( "A_C_0.bam", "A_C_1.bam", "A_C_2.bam", + "A_D_0.bam", "A_D_1.bam", "A_D_2.bam" ) > > targets <- data.frame( + row.names = paste0('Sample_',c(1:6)), + bam = system.file( 'extdata', bamFileNames, package="ASpli" ), + factor1 = c( 'C','C','C','D','D','D'), + subject = c(0, 1, 2, 0, 1, 2)) > > # Read counts from bam files > gbcounts <- gbCounts( features = features, + targets = targets, + minReadLength = 100, maxISize = 50000, + libType="SE", + strandMode=0) Summarizing Sample_1 ETA: 1 min Summarizing Sample_2 ETA: 1 min Summarizing Sample_3 ETA: 1 min Summarizing Sample_4 ETA: 0 min Summarizing Sample_5 ETA: 0 min Summarizing Sample_6 * 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 ERROR, 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/ASpli.Rcheck/00check.log’ for details.
ASpli.Rcheck/00install.out
* installing *source* package ‘ASpli’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘ASpli’ ** testing if installed package keeps a record of temporary installation path * DONE (ASpli)
ASpli.Rcheck/ASpli-Ex.timings
name | user | system | elapsed | |
ASpli-package | 163.827 | 0.878 | 165.021 | |
DUreport | 0 | 0 | 0 | |
DUreport.norm | 0 | 0 | 0 | |
DUreport.offset | 0 | 0 | 0 | |
DUreportBinSplice-method | 0 | 0 | 0 | |
acc_AS | 0 | 0 | 0 | |
acc_DU | 0 | 0 | 0 | |
acc_counts | 0.000 | 0.000 | 0.001 | |
acc_features | 0.230 | 0.004 | 0.234 | |
binGenome | 4.937 | 0.028 | 4.976 | |
containsJunctions-function | 0 | 0 | 0 | |
example_data | 0.000 | 0.000 | 0.001 | |
exportIntegratedSignals | 87.235 | 0.291 | 87.715 | |
exportSplicingReports | 85.224 | 0.344 | 85.711 | |
filterDU-method | 0.000 | 0.000 | 0.001 | |
filterSignals | 0 | 0 | 0 | |
gbCounts | 73.760 | 0.206 | 74.086 | |
gbDUreport-method | 75.614 | 0.248 | 75.998 | |
getConditions-function | 0 | 0 | 0 | |
integrateSignals | 84.859 | 0.271 | 85.287 | |