Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 311/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cfDNAPro 1.13.0 (landing page) Haichao Wang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the cfDNAPro package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cfDNAPro.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. |
Package: cfDNAPro |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cfDNAPro.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cfDNAPro_1.13.0.tar.gz |
StartedAt: 2024-12-23 18:33:09 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 18:34:46 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 96.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: cfDNAPro.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cfDNAPro.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cfDNAPro_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cfDNAPro.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cfDNAPro/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cfDNAPro’ 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘cfDNAPro’ 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 dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘QDNAseq’ * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 1 WARNING See ‘/Users/biocbuild/bbs-3.21-bioc/meat/cfDNAPro.Rcheck/00check.log’ for details.
cfDNAPro.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cfDNAPro ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘cfDNAPro’ ... ** 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 (cfDNAPro)
cfDNAPro.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > library(testthat) > library(cfDNAPro) Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not > > test_check("cfDNAPro") setting default input_type to picard. setting default outfmt to df. setting default input_type to picard. setting default input_type to picard. setting default limit to c(35,135). setting default outfmt to df. setting the mincount to 0. setting default input_type to picard. setting default limit to c(35,135). setting default outfmt to df. Setting default mincount to 0. setting default input_type to picard. setting default input_type to picard. setting default outfmt to df. setting default input_type to picard. setting default input_type to picard. setting default limit to c(35,135). setting default outfmt to df. setting the mincount to 0. setting default input_type to picard. setting default limit to c(35,135). setting default outfmt to df. Setting default mincount to 0. setting default input_type to picard. setting default mincount as 0. setting default horizontal lines: y = 81, 112, 170. setting the mincount to 0. setting the xlim to c(7,13). setting the mincount to 0. setting the xlim to c(7,13). [ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 13 ] > > proc.time() user system elapsed 5.546 0.233 5.813
cfDNAPro.Rcheck/cfDNAPro-Ex.timings
name | user | system | elapsed | |
callMetrics | 0.283 | 0.024 | 0.311 | |
callMode | 0.387 | 0.010 | 0.411 | |
callPeakDistance | 0.052 | 0.001 | 0.053 | |
callSize | 0.040 | 0.001 | 0.041 | |
callValleyDistance | 0.052 | 0.002 | 0.053 | |
examplePath | 0.001 | 0.000 | 0.001 | |
plotAllToOne | 0.068 | 0.003 | 0.071 | |
plotMetrics | 0.247 | 0.006 | 0.253 | |
plotMode | 0.064 | 0.002 | 0.065 | |
plotModeSummary | 0.050 | 0.002 | 0.052 | |
plotPeakDistance | 0.063 | 0.001 | 0.063 | |
plotSingleGroup | 0.231 | 0.003 | 0.234 | |
plotValleyDistance | 0.062 | 0.001 | 0.063 | |
readBam | 0 | 0 | 0 | |
read_bam_insert_metrics | 0 | 0 | 0 | |