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CHECK report for trio on machv2

This page was generated on 2020-10-17 11:59:49 -0400 (Sat, 17 Oct 2020).

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 1835/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.26.0
Holger Schwender
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/trio
Branch: RELEASE_3_11
Last Commit: 884c6df
Last Changed Date: 2020-04-27 14:35:53 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: trio
Version: 3.26.0
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_3.26.0.tar.gz
StartedAt: 2020-10-17 06:03:17 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:07:44 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 266.2 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_3.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/trio.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘3.26.0’
* 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
print.trioFS  8.586  0.049   8.642
trioFS        8.497  0.031   8.533
colGxGPerms   8.286  0.098  14.283
trio.permTest 7.959  0.039   8.063
plot.trioLR   7.269  0.132   8.984
trio.prepare  4.750  0.019   6.739
* 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-3.11-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
allelicTDT0.0450.0060.051
colEMlrt0.1740.0070.181
colGxE0.0160.0020.018
colGxGPerms 8.286 0.09814.283
colPOlrt0.0280.0020.030
colTDTmaxTest0.2410.0100.251
colTDTsam0.0550.0030.059
findLDblocks0.0320.0070.038
getLD0.0350.0060.041
getMatPseudo0.0100.0010.011
lrControl0.0010.0000.001
ped2geno000
plot.LDblocks0.0770.0050.083
plot.getLD0.0430.0040.047
plot.trioLR7.2690.1328.984
poly4root0.0010.0010.002
print.colGxE0.1050.0100.115
print.trioFS8.5860.0498.642
print.trioLR4.7460.0214.771
probTDT0.0900.0320.123
read.pedfile0.0000.0000.001
removeSNPs0.0080.0020.010
scoreTDT0.0190.0030.022
tdt0.0390.0040.043
tdtGxG2.3020.0482.352
trio.check1.4460.0211.470
trio.data0.0110.0020.011
trio.permTest7.9590.0398.063
trio.power0.0250.0020.054
trio.prepare4.7500.0196.739
trio.sim0.4400.0110.452
trioFS8.4970.0318.533
trioLR4.5080.0404.582