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CHECK report for trio on malbec1

This page was generated on 2020-04-15 12:07:58 -0400 (Wed, 15 Apr 2020).

Package 1756/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.24.3
Holger Schwender
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/trio
Branch: RELEASE_3_10
Last Commit: 8f51c41
Last Changed Date: 2020-04-11 14:10:35 -0400 (Sat, 11 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: trio
Version: 3.24.3
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings trio_3.24.3.tar.gz
StartedAt: 2020-04-15 01:49:39 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:52:27 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 168.1 seconds
RetCode: 0
Status:  OK 
CheckDir: trio.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings trio_3.24.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/trio.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘3.24.3’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
print.trioFS  8.880  0.080   9.015
trioFS        8.568  0.036   8.621
trio.permTest 7.464  0.100   7.576
colGxGPerms   6.856  0.020   6.897
plot.trioLR   5.604  0.044   5.701
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/trio.Rcheck/00check.log’
for details.



Installation output

trio.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL trio
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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
   ‘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
allelicTDT0.0240.0000.025
colEMlrt0.1480.0000.151
colGxE0.0120.0000.013
colGxGPerms6.8560.0206.897
colPOlrt0.0240.0000.023
colTDTmaxTest0.0680.0000.070
colTDTsam0.0480.0000.049
findLDblocks0.0320.0000.031
getLD0.0240.0000.023
getMatPseudo0.020.000.02
lrControl0.0000.0000.001
ped2geno0.0000.0000.001
plot.LDblocks0.0720.0000.074
plot.getLD0.0360.0000.033
plot.trioLR5.6040.0445.701
poly4root0.0000.0000.001
print.colGxE0.0480.0000.047
print.trioFS8.8800.0809.015
print.trioLR2.5120.0002.519
probTDT0.0400.0000.039
read.pedfile0.0000.0000.001
removeSNPs0.0080.0000.006
scoreTDT0.0120.0000.010
tdt0.0320.0000.032
tdtGxG1.8720.0001.874
trio.check1.0400.0041.044
trio.data0.0080.0000.008
trio.permTest7.4640.1007.576
trio.power0.0200.0000.019
trio.prepare2.9280.0042.940
trio.sim0.4320.0000.437
trioFS8.5680.0368.621
trioLR2.8840.0002.884