Multiple platform build/check report for BioC 3.10 - CHECK report for trio on merida1

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### Running command:
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###   /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_3.24.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/trio.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘3.24.3’
* 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 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 or elapsed time > 5s
               user system elapsed
print.trioFS  7.373  0.084   7.500
trioFS        6.639  0.075   6.780
colGxGPerms   6.260  0.193   6.490
trio.permTest 5.963  0.071   6.061
plot.trioLR   5.633  0.122   5.802
trioLR        4.059  0.057   5.238
* 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-3.10-bioc/meat/trio.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL trio
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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

name	user	system	elapsed
allelicTDT	0.035	0.004	0.040
colEMlrt	0.138	0.005	0.144
colGxE	0.012	0.001	0.013
colGxGPerms	6.260	0.193	6.490
colPOlrt	0.019	0.001	0.021
colTDTmaxTest	0.062	0.006	0.069
colTDTsam	0.037	0.002	0.039
findLDblocks	0.031	0.006	0.037
getLD	0.024	0.005	0.028
getMatPseudo	0.011	0.002	0.013
lrControl	0.001	0.000	0.000
ped2geno	0	0	0
plot.LDblocks	0.059	0.009	0.069
plot.getLD	0.032	0.002	0.034
plot.trioLR	5.633	0.122	5.802
poly4root	0.001	0.000	0.001
print.colGxE	0.096	0.005	0.106
print.trioFS	7.373	0.084	7.500
print.trioLR	3.582	0.052	3.663
probTDT	0.081	0.015	0.096
read.pedfile	0.000	0.000	0.001
removeSNPs	0.008	0.002	0.010
scoreTDT	0.016	0.002	0.018
tdt	0.033	0.003	0.037
tdtGxG	1.638	0.067	1.715
trio.check	1.009	0.010	1.025
trio.data	0.006	0.001	0.007
trio.permTest	5.963	0.071	6.061
trio.power	0.016	0.000	0.016
trio.prepare	3.177	0.042	3.241
trio.sim	0.365	0.010	0.376
trioFS	6.639	0.075	6.780
trioLR	4.059	0.057	5.238

CHECK report for trio on merida1

Summary

Command output

Installation output

Tests output

Example timings