Multiple platform build/check report for BioC 3.9 - CHECK report for trio on merida2

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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_3.21.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/trio.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘3.21.9’
* 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:
  .Fortran("slogreg", ..., 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
colGxGPerms   42.119  0.246  42.727
print.trioFS  17.360  0.054  17.576
trioFS        16.797  0.074  18.121
tdtGxG        16.215  0.055  17.737
trio.permTest  6.762  0.047   6.868
plot.trioLR    5.965  0.094   6.127
trioLR         3.929  0.050   5.326
* 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-3.9-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’ ...
** 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
* DONE (trio)

Tests output

Example timings

name	user	system	elapsed
allelicTDT	0.033	0.005	0.038
colEMlrt	0.170	0.006	0.179
colGxE	0.008	0.001	0.009
colGxGPerms	42.119	0.246	42.727
colPOlrt	0.026	0.001	0.028
colTDTmaxTest	0.077	0.004	0.082
colTDTsam	0.055	0.003	0.058
findLDblocks	0.037	0.006	0.042
getLD	0.033	0.006	0.039
getMatPseudo	0.010	0.001	0.011
lrControl	0	0	0
ped2geno	0.000	0.001	0.001
plot.LDblocks	0.058	0.005	0.065
plot.getLD	0.046	0.006	0.056
plot.trioLR	5.965	0.094	6.127
poly4root	0.001	0.001	0.002
print.colGxE	0.087	0.005	0.092
print.trioFS	17.360	0.054	17.576
print.trioLR	4.039	0.036	4.108
probTDT	0.110	0.019	0.129
read.pedfile	0	0	0
removeSNPs	0.010	0.002	0.011
scoreTDT	0.012	0.001	0.014
tdt	0.197	0.002	0.202
tdtGxG	16.215	0.055	17.737
trio.check	0.965	0.004	0.976
trio.data	0.007	0.001	0.008
trio.permTest	6.762	0.047	6.868
trio.power	0.022	0.002	0.024
trio.prepare	3.805	0.055	3.905
trio.sim	0.352	0.004	0.356
trioFS	16.797	0.074	18.121
trioLR	3.929	0.050	5.326

CHECK report for trio on merida2

Summary

Command output

Installation output

Tests output

Example timings