Multiple platform build/check report for BioC 3.9 - CHECK report for trio on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings trio_3.21.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/trio.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘3.21.9’
* 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 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   42.354  0.035  43.004
trioFS        16.294  0.028  18.160
print.trioFS  15.061  0.004  15.802
tdtGxG        13.307  0.000  13.876
trio.permTest  7.379  0.000   7.994
* 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-3.9-bioc/meat/trio.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL trio
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* installing to library ‘/home/biocbuild/bbs-3.9-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

name	user	system	elapsed
allelicTDT	0.025	0.012	0.037
colEMlrt	0.15	0.00	0.15
colGxE	0.012	0.000	0.013
colGxGPerms	42.354	0.035	43.004
colPOlrt	0.014	0.000	0.015
colTDTmaxTest	0.038	0.008	0.046
colTDTsam	0.039	0.000	0.040
findLDblocks	0.021	0.000	0.021
getLD	0.015	0.000	0.016
getMatPseudo	0.211	0.000	0.212
lrControl	0	0	0
ped2geno	0	0	0
plot.LDblocks	0.046	0.000	0.046
plot.getLD	0.029	0.000	0.030
plot.trioLR	4.484	0.020	4.526
poly4root	0.000	0.000	0.001
print.colGxE	0.045	0.000	0.045
print.trioFS	15.061	0.004	15.802
print.trioLR	3.764	0.000	4.116
probTDT	0.062	0.004	0.082
read.pedfile	0.000	0.000	0.001
removeSNPs	0.006	0.004	0.010
scoreTDT	0.015	0.000	0.015
tdt	0.268	0.004	0.367
tdtGxG	13.307	0.000	13.876
trio.check	0.633	0.000	0.632
trio.data	0.006	0.000	0.005
trio.permTest	7.379	0.000	7.994
trio.power	0.012	0.000	0.012
trio.prepare	2.542	0.000	2.542
trio.sim	0.295	0.000	0.295
trioFS	16.294	0.028	18.160
trioLR	2.322	0.000	2.322

CHECK report for trio on malbec2

Summary

Command output

Installation output

Tests output

Example timings