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This page was generated on 2025-08-21 11:43 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2245/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.46.0  (landing page)
Holger Schwender
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/trio
git_branch: RELEASE_3_21
git_last_commit: db20b0d
git_last_commit_date: 2025-04-15 10:25:51 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for trio on kunpeng2

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: 3.46.0
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_3.46.0.tar.gz
StartedAt: 2025-08-19 15:07:26 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 15:10:24 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 178.1 seconds
RetCode: 0
Status:   OK  
CheckDir: trio.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_3.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/trio.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trio’ version ‘3.46.0’
* 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  6.292  0.096   6.404
trio.permTest 6.110  0.084   6.210
trioFS        6.081  0.043   6.138
colGxGPerms   5.738  0.172   5.928
plot.trioLR   4.997  0.215   5.236
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘trio’ ...
** this is package ‘trio’ version ‘3.46.0’
** 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
allelicTDT0.0330.0000.034
colEMlrt0.1490.0000.149
colGxE0.0090.0000.009
colGxGPerms5.7380.1725.928
colNtrios0.0190.0000.020
colPOlrt0.0180.0000.018
colTDTmaxTest0.0770.0000.077
colTDTsam0.0340.0120.048
findLDblocks0.0310.0000.031
getLD0.0300.0000.031
getMatPseudo0.0070.0000.008
lrControl0.0000.0000.001
ntrios2Dom0.0060.0000.006
ped2geno000
plot.LDblocks0.0620.0060.069
plot.getLD0.0460.0000.047
plot.trioLR4.9970.2155.236
poly4root0.0010.0000.001
print.colGxE0.0610.0000.061
print.trioFS6.2920.0966.404
print.trioLR3.4710.0043.485
probTDT0.0340.0080.041
read.pedfile000
removeSNPs0.0070.0000.006
scoreTDT0.0090.0020.011
tdt0.0340.0010.034
tdtGxG1.5780.0001.582
trio.check1.0120.0001.015
trio.data0.0050.0000.006
trio.permTest6.1100.0846.210
trio.power0.0140.0000.014
trio.prepare3.2480.0003.258
trio.sim0.4330.0030.437
trioFS6.0810.0436.138
trioLR3.3850.0003.395