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_3.21.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/trio.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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   56.850  0.666  57.519
print.trioFS  21.704  0.088  23.364
trioFS        20.623  0.095  22.058
tdtGxG        18.292  0.079  19.049
trio.permTest  8.764  0.063   8.944
plot.trioLR    5.959  0.146   6.174
* 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	0.029	0.006	0.036
colEMlrt	0.125	0.009	0.134
colGxE	0.014	0.002	0.015
colGxGPerms	56.850	0.666	57.519
colPOlrt	0.017	0.001	0.018
colTDTmaxTest	0.065	0.013	0.079
colTDTsam	0.047	0.003	0.050
findLDblocks	0.037	0.011	0.047
getLD	0.037	0.027	0.065
getMatPseudo	0.011	0.003	0.014
lrControl	0.000	0.001	0.000
ped2geno	0.000	0.001	0.001
plot.LDblocks	0.075	0.015	0.090
plot.getLD	0.055	0.016	0.072
plot.trioLR	5.959	0.146	6.174
poly4root	0.000	0.000	0.001
print.colGxE	0.101	0.009	0.109
print.trioFS	21.704	0.088	23.364
print.trioLR	4.148	0.053	4.202
probTDT	0.114	0.035	0.150
read.pedfile	0.000	0.001	0.000
removeSNPs	0.009	0.003	0.011
scoreTDT	0.018	0.004	0.021
tdt	0.310	0.005	0.315
tdtGxG	18.292	0.079	19.049
trio.check	1.731	0.011	2.905
trio.data	0.008	0.002	0.023
trio.permTest	8.764	0.063	8.944
trio.power	0.015	0.001	0.017
trio.prepare	3.974	0.056	4.184
trio.sim	0.523	0.010	0.900
trioFS	20.623	0.095	22.058
trioLR	3.695	0.130	3.825

CHECK report for trio on celaya2

Summary

Command output

Installation output

Tests output

Example timings