Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-23 12:08 -0400 (Sat, 23 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 2225/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
trio 3.47.0 (landing page) Holger Schwender
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the trio package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/trio.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: trio |
Version: 3.47.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings trio_3.47.0.tar.gz |
StartedAt: 2025-08-22 13:26:01 -0000 (Fri, 22 Aug 2025) |
EndedAt: 2025-08-22 13:29:13 -0000 (Fri, 22 Aug 2025) |
EllapsedTime: 192.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: trio.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings trio_3.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/trio.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘trio/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘trio’ version ‘3.47.0’ * 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 ‘trio’ 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function call to a different package: .C("clogreg", ..., PACKAGE = "LogicReg") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE read.pedfile: no visible binding for global variable ‘..ids.select’ Undefined global functions or variables: ..ids.select * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed print.trioFS 6.278 0.079 7.439 trioFS 5.951 0.044 6.590 trio.permTest 5.459 0.032 5.759 colGxGPerms 5.140 0.020 5.974 plot.trioLR 4.693 0.143 5.189 * 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 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/trio.Rcheck/00check.log’ for details.
trio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL trio ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘trio’ ... ** this is package ‘trio’ version ‘3.47.0’ ** using staged installation ** R ** data ** 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 (trio)
trio.Rcheck/trio-Ex.timings
name | user | system | elapsed | |
allelicTDT | 0.027 | 0.000 | 0.027 | |
colEMlrt | 0.131 | 0.000 | 0.132 | |
colGxE | 0.008 | 0.000 | 0.009 | |
colGxGPerms | 5.140 | 0.020 | 5.974 | |
colNtrios | 0.010 | 0.008 | 0.019 | |
colPOlrt | 0.017 | 0.000 | 0.018 | |
colTDTmaxTest | 0.072 | 0.000 | 0.072 | |
colTDTsam | 0.036 | 0.004 | 0.040 | |
findLDblocks | 0.184 | 0.000 | 0.184 | |
getLD | 0.016 | 0.000 | 0.015 | |
getMatPseudo | 0.007 | 0.000 | 0.007 | |
lrControl | 0.001 | 0.000 | 0.000 | |
ntrios2Dom | 0.006 | 0.000 | 0.006 | |
ped2geno | 0 | 0 | 0 | |
plot.LDblocks | 0.060 | 0.000 | 0.061 | |
plot.getLD | 0.03 | 0.00 | 0.03 | |
plot.trioLR | 4.693 | 0.143 | 5.189 | |
poly4root | 0.000 | 0.000 | 0.001 | |
print.colGxE | 0.068 | 0.000 | 0.070 | |
print.trioFS | 6.278 | 0.079 | 7.439 | |
print.trioLR | 3.368 | 0.004 | 3.382 | |
probTDT | 0.036 | 0.004 | 0.040 | |
read.pedfile | 0.001 | 0.000 | 0.000 | |
removeSNPs | 0.002 | 0.004 | 0.006 | |
scoreTDT | 0.011 | 0.000 | 0.011 | |
tdt | 0.034 | 0.000 | 0.033 | |
tdtGxG | 1.682 | 0.016 | 1.702 | |
trio.check | 0.924 | 0.012 | 0.939 | |
trio.data | 0.005 | 0.000 | 0.005 | |
trio.permTest | 5.459 | 0.032 | 5.759 | |
trio.power | 0.013 | 0.000 | 0.022 | |
trio.prepare | 3.166 | 0.000 | 3.626 | |
trio.sim | 0.333 | 0.000 | 0.335 | |
trioFS | 5.951 | 0.044 | 6.590 | |
trioLR | 3.196 | 0.000 | 3.227 | |