Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:47 -0400 (Tue, 27 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" | 4415 |
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 1476/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
panelcn.mops 1.27.0 (landing page) Gundula Povysil
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the panelcn.mops package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/panelcn.mops.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: panelcn.mops |
Version: 1.27.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:panelcn.mops.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings panelcn.mops_1.27.0.tar.gz |
StartedAt: 2024-08-27 07:34:18 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 07:37:09 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 171.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: panelcn.mops.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:panelcn.mops.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings panelcn.mops_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/panelcn.mops.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 ‘panelcn.mops/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘panelcn.mops’ version ‘1.27.0’ * 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 ‘panelcn.mops’ 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 ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ 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: OK
panelcn.mops.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL panelcn.mops ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘panelcn.mops’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (panelcn.mops)
panelcn.mops.Rcheck/tests/runTests.Rout
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. > BiocGenerics:::testPackage("panelcn.mops") Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'cn.mops' The following object is masked from 'package:S4Vectors': params Calculating results for sample(s) SAMPLE1.bam SAMPLE1.bam Building table... SAMPLE1.bam Finished naming without chr prefix chosen, but BED contains chr -> removing chr Analyzing sample(s) SAMPLE1.bam new sampleThresh 235.95 Cannot use exon PMS2.E2.chr7.6045492.6045693 Cannot use exon CHEK2.E15.chr22.29083854.29084005 Cannot use exon CHEK2.E14.chr22.29085092.29085234 Cannot use exon CHEK2.E13.chr22.29089989.29090136 Analyzing sample SAMPLE1.bam "corrThresh" is set to 0.99 "maxControls" is set to 25 1 0.997060493255309 0.996941831461954 0.996599322273787 0.995380799421952 0.930827189241917 Low correlation. Selected 5 out of 5 controls: SAMPLE4.bam SAMPLE3.bam SAMPLE6.bam SAMPLE2.bam SAMPLE5.bam Normalizing... Removed bad control sample(s) SAMPLE5.bam Normalizing again... Remaining samples: SAMPLE1.bam Remaining samples: SAMPLE4.bam Remaining samples: SAMPLE3.bam Remaining samples: SAMPLE6.bam Remaining samples: SAMPLE2.bam Low quality exon(s): 7_6012999_6013204 7_6017188_6017419 7_6018196_6018358 17_29422297_29422418 Computing results... Creating CNVDetectionResult Finished genepanelcn.mops RUNIT TEST PROTOCOL -- Tue Aug 27 07:37:06 2024 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : panelcn.mops RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 5.756 0.256 6.008
panelcn.mops.Rcheck/panelcn.mops-Ex.timings
name | user | system | elapsed | |
control | 0.087 | 0.000 | 0.087 | |
countBamListInGRanges | 0.012 | 0.000 | 0.013 | |
countWindows | 0.008 | 0.004 | 0.012 | |
createResultTable | 0.177 | 0.004 | 0.181 | |
getWindows | 0.004 | 0.004 | 0.008 | |
panelcn.mops | 0.773 | 0.036 | 0.811 | |
plotBoxplot | 0.050 | 0.000 | 0.049 | |
read.width | 0.001 | 0.000 | 0.001 | |
resultlist | 0.029 | 0.004 | 0.034 | |
runPanelcnMops | 0.904 | 0.008 | 0.914 | |
splitROIs | 0.123 | 0.000 | 0.124 | |
test | 0.017 | 0.000 | 0.018 | |