Multiple platform build/check report for BioC 3.9 - CHECK report for trio on celaya2

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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_3.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/trio.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘3.22.0’
* 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:
  .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   59.834  0.691  60.942
print.trioFS  22.600  0.117  24.429
trioFS        21.011  0.146  21.158
tdtGxG        20.036  0.134  22.086
trio.permTest  9.354  0.084   9.437
plot.trioLR    6.703  0.186   6.897
print.trioLR   5.283  0.080   5.418
trio.prepare   4.481  0.119   6.458
* 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’ ...
** 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	0.044	0.008	0.051
colEMlrt	0.204	0.017	0.221
colGxE	0.010	0.002	0.013
colGxGPerms	59.834	0.691	60.942
colPOlrt	0.021	0.003	0.023
colTDTmaxTest	0.067	0.013	0.080
colTDTsam	0.047	0.010	0.057
findLDblocks	0.025	0.006	0.032
getLD	0.023	0.011	0.034
getMatPseudo	0.016	0.010	0.025
lrControl	0	0	0
ped2geno	0.000	0.000	0.001
plot.LDblocks	0.060	0.005	0.066
plot.getLD	0.047	0.014	0.062
plot.trioLR	6.703	0.186	6.897
poly4root	0.001	0.000	0.002
print.colGxE	0.106	0.009	0.115
print.trioFS	22.600	0.117	24.429
print.trioLR	5.283	0.080	5.418
probTDT	0.081	0.023	0.105
read.pedfile	0	0	0
removeSNPs	0.008	0.004	0.012
scoreTDT	0.017	0.005	0.023
tdt	0.231	0.006	0.237
tdtGxG	20.036	0.134	22.086
trio.check	1.377	0.011	1.388
trio.data	0.008	0.002	0.009
trio.permTest	9.354	0.084	9.437
trio.power	0.041	0.005	0.046
trio.prepare	4.481	0.119	6.458
trio.sim	0.369	0.011	0.380
trioFS	21.011	0.146	21.158
trioLR	4.303	0.069	4.372

CHECK report for trio on celaya2

Summary

Command output

Installation output

Tests output

Example timings