Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2198/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
trio 3.44.0 (landing page) Holger Schwender
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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. |
Package: trio |
Version: 3.44.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:trio.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings trio_3.44.0.tar.gz |
StartedAt: 2024-12-20 06:59:45 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:02:43 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 177.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: trio.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:trio.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings trio_3.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/trio.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'trio/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'trio' version '3.44.0' * 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 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 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 .onAttach: no visible global function definition for 'winMenuAdd' .onAttach: no visible global function definition for 'winMenuAddItem' Undefined global functions or variables: winMenuAdd winMenuAddItem Consider adding importFrom("utils", "winMenuAdd", "winMenuAddItem") to your NAMESPACE file. * 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 sizes of PDF files under 'inst/doc' ... 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 8.37 0.15 8.54 trioFS 7.48 0.26 7.76 trio.permTest 7.32 0.17 7.48 colGxGPerms 5.38 0.30 5.69 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/trio.Rcheck/00check.log' for details.
trio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL trio ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'trio' ... ** 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 | 0.05 | 0.00 | 0.05 | |
colEMlrt | 0.08 | 0.01 | 0.10 | |
colGxE | 0.01 | 0.00 | 0.01 | |
colGxGPerms | 5.38 | 0.30 | 5.69 | |
colPOlrt | 0.04 | 0.00 | 0.03 | |
colTDTmaxTest | 0.06 | 0.01 | 0.08 | |
colTDTsam | 0.25 | 0.02 | 0.28 | |
findLDblocks | 0.01 | 0.01 | 0.03 | |
getLD | 0.02 | 0.02 | 0.03 | |
getMatPseudo | 0 | 0 | 0 | |
lrControl | 0 | 0 | 0 | |
ped2geno | 0.00 | 0.02 | 0.02 | |
plot.LDblocks | 0.03 | 0.01 | 0.05 | |
plot.getLD | 0.03 | 0.02 | 0.04 | |
plot.trioLR | 4.13 | 0.25 | 4.39 | |
poly4root | 0 | 0 | 0 | |
print.colGxE | 0.06 | 0.00 | 0.07 | |
print.trioFS | 8.37 | 0.15 | 8.54 | |
print.trioLR | 3.10 | 0.10 | 3.19 | |
probTDT | 0.06 | 0.00 | 0.06 | |
read.pedfile | 0 | 0 | 0 | |
removeSNPs | 0.02 | 0.00 | 0.02 | |
scoreTDT | 0.01 | 0.00 | 0.02 | |
tdt | 0.03 | 0.00 | 0.03 | |
tdtGxG | 1.60 | 0.03 | 1.62 | |
trio.check | 0.56 | 0.05 | 0.61 | |
trio.data | 0 | 0 | 0 | |
trio.permTest | 7.32 | 0.17 | 7.48 | |
trio.power | 0.00 | 0.01 | 0.02 | |
trio.prepare | 2.81 | 0.05 | 2.86 | |
trio.sim | 0.44 | 0.02 | 0.45 | |
trioFS | 7.48 | 0.26 | 7.76 | |
trioLR | 2.75 | 0.02 | 2.77 | |