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This page was generated on 2025-08-04 12:13 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 2219/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.47.0  (landing page)
Holger Schwender
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/trio
git_branch: devel
git_last_commit: ebc6338
git_last_commit_date: 2025-04-15 10:25:51 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for trio on taishan

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.

raw results


Summary

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: 2025-08-01 12:30:18 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 12:33:11 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 173.1 seconds
RetCode: 0
Status:   OK  
CheckDir: trio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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  6.302  0.095   6.437
trioFS        6.087  0.094   6.221
trio.permTest 5.902  0.123   6.062
colGxGPerms   5.306  0.047   5.386
plot.trioLR   5.145  0.142   5.333
* 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.


Installation output

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)

Tests output


Example timings

trio.Rcheck/trio-Ex.timings

nameusersystemelapsed
allelicTDT0.0250.0040.029
colEMlrt0.1370.0040.141
colGxE0.0090.0000.009
colGxGPerms5.3060.0475.386
colNtrios0.0150.0040.020
colPOlrt0.0170.0000.017
colTDTmaxTest0.0670.0040.071
colTDTsam0.0380.0040.043
findLDblocks0.0310.0000.031
getLD0.0170.0000.017
getMatPseudo0.0080.0000.008
lrControl0.0000.0000.001
ntrios2Dom0.0060.0000.006
ped2geno000
plot.LDblocks0.0650.0000.066
plot.getLD0.0300.0000.031
plot.trioLR5.1450.1425.333
poly4root0.0010.0000.000
print.colGxE0.0570.0040.060
print.trioFS6.3020.0956.437
print.trioLR3.4150.0703.515
probTDT0.0470.0040.051
read.pedfile000
removeSNPs0.0060.0000.006
scoreTDT0.0120.0000.012
tdt0.0250.0000.026
tdtGxG1.5060.0041.519
trio.check1.0280.0161.057
trio.data0.0050.0000.005
trio.permTest5.9020.1236.062
trio.power0.0140.0000.014
trio.prepare3.2310.0243.279
trio.sim0.3440.0040.350
trioFS6.0870.0946.221
trioLR3.2930.0233.330