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CHECK report for trio on merida1

This page was generated on 2021-05-06 12:37:16 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the trio package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1899/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.28.0  (landing page)
Holger Schwender
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/trio
Branch: RELEASE_3_12
Last Commit: cf7985a
Last Changed Date: 2020-10-27 10:52:11 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: trio
Version: 3.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:trio.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings trio_3.28.0.tar.gz
StartedAt: 2021-05-06 07:02:50 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:06:37 -0400 (Thu, 06 May 2021)
EllapsedTime: 226.9 seconds
RetCode: 0
Status:   OK  
CheckDir: trio.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:trio.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings trio_3.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/trio.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trio’ version ‘3.28.0’
* 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 R 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 ... 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 ... 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 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
colGxGPerms   7.333  0.151   7.493
trioFS        7.120  0.029   7.155
trio.permTest 6.622  0.025   6.657
print.trioFS  6.539  0.055   6.601
plot.trioLR   5.839  0.132   5.980
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/trio.Rcheck/00check.log’
for details.



Installation output

trio.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL trio
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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
   ‘trio.Rnw’ 
** 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
allelicTDT0.0370.0040.041
colEMlrt0.1540.0050.160
colGxE0.0100.0020.011
colGxGPerms7.3330.1517.493
colPOlrt0.0220.0020.025
colTDTmaxTest0.0580.0060.065
colTDTsam0.0450.0020.047
findLDblocks0.0280.0020.032
getLD0.0310.0040.035
getMatPseudo0.0090.0010.010
lrControl000
ped2geno000
plot.LDblocks0.0700.0030.075
plot.getLD0.0430.0060.050
plot.trioLR5.8390.1325.980
poly4root0.0010.0000.001
print.colGxE0.0860.0080.093
print.trioFS6.5390.0556.601
print.trioLR3.4800.0313.521
probTDT0.0670.0250.093
read.pedfile0.0000.0000.001
removeSNPs0.0080.0010.009
scoreTDT0.0130.0010.013
tdt0.0270.0020.030
tdtGxG1.5360.0431.579
trio.check1.1530.0081.163
trio.data0.0080.0010.009
trio.permTest6.6220.0256.657
trio.power0.0250.0010.026
trio.prepare3.6690.0143.687
trio.sim0.4140.0040.418
trioFS7.1200.0297.155
trioLR3.6600.0173.682