Package: trio

Version: 3.22.0

Command: /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_3.22.0.tar.gz

StartedAt: 2019-10-16 05:34:45 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:38:40 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 235.2 seconds

RetCode: 0

Status:  OK

CheckDir: trio.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_3.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/trio.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘3.22.0’
* 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 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   44.470  0.036  46.574
tdtGxG        16.242  0.008  16.740
print.trioFS  15.945  0.004  16.737
trioFS        13.962  0.004  13.968
trio.permTest  6.785  0.008   7.142
plot.trioLR    4.993  0.083   5.220
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL trio
###
##############################################################################
##############################################################################


* 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)

name	user	system	elapsed
allelicTDT	0.023	0.000	0.023
colEMlrt	0.089	0.004	0.093
colGxE	0.008	0.000	0.009
colGxGPerms	44.470	0.036	46.574
colPOlrt	0.023	0.000	0.024
colTDTmaxTest	0.063	0.008	0.070
colTDTsam	0.048	0.000	0.049
findLDblocks	0.036	0.004	0.040
getLD	0.023	0.000	0.024
getMatPseudo	0.012	0.000	0.012
lrControl	0.001	0.000	0.000
ped2geno	0.001	0.000	0.000
plot.LDblocks	0.081	0.000	0.080
plot.getLD	0.041	0.008	0.050
plot.trioLR	4.993	0.083	5.220
poly4root	0.001	0.000	0.001
print.colGxE	0.064	0.000	0.064
print.trioFS	15.945	0.004	16.737
print.trioLR	3.457	0.036	3.842
probTDT	0.065	0.004	0.136
read.pedfile	0	0	0
removeSNPs	0.009	0.000	0.026
scoreTDT	0.012	0.004	0.040
tdt	0.230	0.008	0.259
tdtGxG	16.242	0.008	16.740
trio.check	1.127	0.004	1.327
trio.data	0.008	0.000	0.032
trio.permTest	6.785	0.008	7.142
trio.power	0.012	0.000	0.012
trio.prepare	2.207	0.000	2.208
trio.sim	0.314	0.000	0.314
trioFS	13.962	0.004	13.968
trioLR	2.371	0.000	2.371