Package: FamAgg

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FamAgg.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FamAgg_1.12.0.tar.gz

StartedAt: 2019-10-16 02:44:59 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:47:44 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 164.3 seconds

RetCode: 0

Status:  OK

CheckDir: FamAgg.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FamAgg.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FamAgg_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/FamAgg.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 ‘FamAgg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FamAgg’ version ‘1.12.0’
* 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 ‘FamAgg’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: OK

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FamAgg
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘FamAgg’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘pedigree’ in package ‘FamAgg’
in method for ‘countGenerations’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘countGenerations’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘estimateGenerations’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘estimateGenerations’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘findFounders’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘findFounders’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘generationsFrom’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘generationsFrom’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getAncestors’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getAncestors’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getChildren’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getChildren’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getCommonAncestor’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getCommonAncestor’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getMissingMate’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getMissingMate’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getSiblings’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getSiblings’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getAll’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getAll’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getExternalMatched’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getExternalMatched’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getGenerationMatched’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getGenerationMatched’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getGenerationSexMatched’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getGenerationSexMatched’ with signature ‘"pedigree"’: no definition for class “pedigree”
in method for ‘getSexMatched’ with signature ‘"pedigreeList"’: no definition for class “pedigreeList”
in method for ‘getSexMatched’ with signature ‘"pedigree"’: no definition for class “pedigree”
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (FamAgg)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("FamAgg")

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'FamAgg'

The following object is masked from 'package:igraph':

    cliques

The following object is masked from 'package:kinship2':

    pedigree

Reading pedigree information from file  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/FamAgg/txt/minnbreastsub.txt ...Reading pedigree information from file  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/FamAgg/txt/minnbreastsub.txt ...OK

Generating the kinship matrix...OK

Reading pedigree information from file  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/FamAgg/txt/minnbreastsub.txt ...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Reading pedigree information from file  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/FamAgg/txt/minnbreastsub.txt ...OK

Reading pedigree information from file  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/FamAgg/txt/minnbreastsub.txt ...OK

Generating the kinship matrix...OK

Reading pedigree information from file  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/FamAgg/txt/minnbreastsub.ped.gz ...OK

Generating the kinship matrix...OK

Reading pedigree information from file  /Library/Frameworks/R.framework/Versions/3.6/Resources/library/FamAgg/txt/minnbreastsub-bad.ped.gz ...Generating the kinship matrix...OK

Generating the kinship matrix...OK

Removing singletons... none present.
Removing singletons... none present.
Removing singletons... none present.
Removing singletons... 1 removed.
Removing singletons... 11 removed.
Removing singletons... 11 removed.
Generating the kinship matrix...OK

851 of in total 851 trait values can be matched to IDs in the pedigree.
Generating the kinship matrix...OK

851 of in total 851 trait values can be matched to IDs in the pedigree.
851 of in total 851 trait values can be matched to IDs in the pedigree.
Generating the kinship matrix...OK

851 of in total 851 trait values can be matched to IDs in the pedigree.
Generating the kinship matrix...OK

Reading pedigree information from file  /tmp/RtmpRl92Q3/filec7821188b8f2.ped ...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

851 of in total 851 trait values can be matched to IDs in the pedigree.
38 of in total 38 trait values can be matched to IDs in the pedigree.
100 of in total 100 trait values can be matched to IDs in the pedigree.
100 of in total 100 trait values can be matched to IDs in the pedigree.
Generating the kinship matrix...Generating the kinship matrix...Generating the kinship matrix...OK

851 of in total 851 trait values can be matched to IDs in the pedigree.
851 of in total 851 trait values can be matched to IDs in the pedigree.
851 of in total 851 trait values can be matched to IDs in the pedigree.
851 of in total 851 trait values can be matched to IDs in the pedigree.
851 of in total 851 trait values can be matched to IDs in the pedigree.
851 of in total 851 trait values can be matched to IDs in the pedigree.
851 of in total 851 trait values can be matched to IDs in the pedigree.
Generating the kinship matrix...OK

Generating the kinship matrix...OK

1182 of in total 1182 trait values can be matched to IDs in the pedigree.
Cleaning data set (got in total 1182 individuals):
 * not phenotyped individuals... 427 removed.
 * individuals with missing time in strata... 187 removed.
 * singletons (also caused by previous subsetting)... 144 removed.
Done
Cleaning data set (got in total 1182 individuals):
 * not phenotyped individuals... 427 removed.
 * individuals with missing time in strata... 187 removed.
 * singletons (also caused by previous subsetting)... 144 removed.
Done
Cleaning data set (got in total 1182 individuals):
 * not phenotyped individuals... 427 removed.
 * individuals with missing time in strata... 187 removed.
 * singletons (also caused by previous subsetting)... 144 removed.
Done
Cleaning data set (got in total 1182 individuals):
 * not phenotyped individuals... 427 removed.
 * individuals with missing time in strata... 187 removed.
 * singletons (also caused by previous subsetting)... 144 removed.
Done
Cleaning data set (got in total 1182 individuals):
 * not phenotyped individuals... 427 removed.
 * individuals with missing time in strata... 187 removed.
 * singletons (also caused by previous subsetting)... 144 removed.
Done
Cleaning data set (got in total 1182 individuals):
 * not phenotyped individuals... 427 removed.
 * individuals with missing time in strata... 187 removed.
 * singletons (also caused by previous subsetting)... 144 removed.
Done
Generating the kinship matrix...OK

Removing singletons... 69 removed.
Cleaning data set (got in total 231 individuals):
 * not phenotyped individuals among selected controls... 52 removed.
Done
Removing singletons... 69 removed.
Cleaning data set (got in total 231 individuals):
 * not phenotyped individuals among selected controls... 25 removed.
Done
Removing singletons... 69 removed.
Cleaning data set (got in total 231 individuals):
 * affected individuals without valid strata values... none present.
 * not phenotyped individuals among selected controls... 25 removed.
 * control individuals without valid strata values... none present.
Done
300 of in total 300 trait values can be matched to IDs in the pedigree.
Removing singletons... 69 removed.
Cleaning data set (got in total 29 individuals):
 * not phenotyped individuals among selected controls... none present.
Done
Cleaning data set (got in total 27 individuals):
Cleaning data set (got in total 33 individuals):
Cleaning data set (got in total 30 individuals):
 * not phenotyped individuals among selected controls... 1 removed.
Done
Cleaning data set (got in total 62 individuals):
 * not phenotyped individuals among selected controls... 31 removed.
Done
Cleaning data set (got in total 50 individuals):
Removing singletons... 69 removed.
Cleaning data set (got in total 29 individuals):
 * not phenotyped individuals among selected controls... none present.
Done
Cleaning data set (got in total 27 individuals):
Cleaning data set (got in total 33 individuals):
Cleaning data set (got in total 30 individuals):
 * not phenotyped individuals among selected controls... 1 removed.
Done
Cleaning data set (got in total 62 individuals):
 * not phenotyped individuals among selected controls... 3 removed.
Done
Cleaning data set (got in total 50 individuals):
Removing singletons... 69 removed.
Cleaning data set (got in total 29 individuals):
 * not phenotyped individuals among selected controls... none present.
Done
Cleaning data set (got in total 27 individuals):
Cleaning data set (got in total 33 individuals):
Cleaning data set (got in total 30 individuals):
 * not phenotyped individuals among selected controls... none present.
Done
Cleaning data set (got in total 62 individuals):
 * not phenotyped individuals among selected controls... 14 removed.
Done
Cleaning data set (got in total 50 individuals):
Removing singletons... 69 removed.
Cleaning data set (got in total 29 individuals):
 * not phenotyped individuals among selected controls... none present.
Done
Cleaning data set (got in total 27 individuals):
Cleaning data set (got in total 33 individuals):
Cleaning data set (got in total 30 individuals):
 * not phenotyped individuals among selected controls... none present.
Done
Cleaning data set (got in total 62 individuals):
 * not phenotyped individuals among selected controls... 2 removed.
Done
Cleaning data set (got in total 50 individuals):
Did not plot the following people: 160 164 167 168 169 170 171 172 173 174 
Removing singletons... 69 removed.
Cleaning data set (got in total 29 individuals):
 * affected individuals without valid strata values... none present.
 * not phenotyped individuals among selected controls... none present.
 * control individuals without valid strata values... none present.
Done
Cleaning data set (got in total 27 individuals):
 * affected individuals without valid strata values... none present.
Cleaning data set (got in total 33 individuals):
 * affected individuals without valid strata values... none present.
Cleaning data set (got in total 30 individuals):
 * affected individuals without valid strata values... none present.
 * not phenotyped individuals among selected controls... 1 removed.
 * control individuals without valid strata values... none present.
Done
Cleaning data set (got in total 62 individuals):
 * affected individuals without valid strata values... none present.
 * not phenotyped individuals among selected controls... 31 removed.
 * control individuals without valid strata values... 3 removed.
Done
Cleaning data set (got in total 50 individuals):
 * affected individuals without valid strata values... none present.
Removing singletons... 69 removed.
Cleaning data set (got in total 29 individuals):
 * affected individuals without valid strata values... none present.
 * not phenotyped individuals among selected controls... none present.
 * control individuals without valid strata values... none present.
Done
Cleaning data set (got in total 27 individuals):
 * affected individuals without valid strata values... none present.
Cleaning data set (got in total 33 individuals):
 * affected individuals without valid strata values... none present.
Cleaning data set (got in total 30 individuals):
 * affected individuals without valid strata values... none present.
 * not phenotyped individuals among selected controls... 1 removed.
 * control individuals without valid strata values... none present.
Done
Cleaning data set (got in total 62 individuals):
 * affected individuals without valid strata values... none present.
 * not phenotyped individuals among selected controls... 3 removed.
 * control individuals without valid strata values... none present.
Done
Cleaning data set (got in total 50 individuals):
 * affected individuals without valid strata values... none present.
gap version 1.2.1
Cleaning data set (got in total 300 individuals):
 * not phenotyped individuals among selected controls... 92 removed.
Done
Removing singletons... 69 removed.
Cleaning data set (got in total 231 individuals):
 * not phenotyped individuals among selected controls... 52 removed.
Done
Removing singletons... 69 removed.
Generating the kinship matrix...OK

Transforming startDate into Date format...OK
Transforming startDate into Date format...OK
'endDate' is assumed to specify, for each individual, either the end year of the study, the individual's death date or the individual's incidence date.
Transforming endDate into Date format...OK
Transforming startDate into Date format...OK
Transforming endDate into Date format...OK
Transforming incidenceDate into Date format...OK
Transforming startDate into Date format...OK
Transforming endDate into Date format...OK
Transforming incidenceDate into Date format...OK
Transforming deathDate into Date format...OK
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * individuals without valid strata values... none present.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals... 245 removed.
 * individuals with unknown time at risk... 156 removed.
 * singletons (also caused by previous subsetting)... 106 removed.
Done
Generating the kinship matrix...OK

Cleaning data set (got in total 873 individuals):
 * not phenotyped individuals...
 410 removed
Done
Removing singletons... none present.
Removing singletons... 1 removed.
Cleaning data set (got in total 873 individuals):
 * not phenotyped individuals...
 410 removed
Done
Cleaning data set (got in total 873 individuals):
 * not phenotyped individuals...
 410 removed
Done
873 of in total 873 trait values can be matched to IDs in the pedigree.
Cleaning data set (got in total 873 individuals):
 * not phenotyped individuals...
 410 removed
Done
Generating the kinship matrix...OK

Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals...
 245 removed
Done
851 of in total 851 trait values can be matched to IDs in the pedigree.
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals...
 637 removed
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals...
 245 removed
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals...
 245 removed
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals...
 245 removed
 * unaffected individuals without valid strata values... none present.
 * affected individuals without valid strata values... none present.
Done
Cleaning data set (got in total 419 individuals):
 * not phenotyped individuals...
 173 removed
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals...
 245 removed
 * unaffected individuals without valid strata values... 360 removed.
 * affected individuals without valid strata values... 37 removed.
Done
Cleaning data set (got in total 851 individuals):
 * not phenotyped individuals...
 245 removed
Done
Plotting backend: ks2paint.
Removing singletons... none present.
Generating the kinship matrix...OK

851 of in total 851 trait values can be matched to IDs in the pedigree.
Did not plot the following people: 30 31 32 33 34 35 36 37 38 39 40 41 42 43 
Did not plot the following people: 30 31 32 33 34 35 36 37 38 39 40 41 42 43 
Did not plot the following people: 30 31 32 33 34 35 36 37 38 39 40 41 42 43 
Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Generating the kinship matrix...OK

Removing singletons... 77 removed.
Generating the kinship matrix...OK

310 of in total 310 trait values can be matched to IDs in the pedigree.
Removing singletons... 77 removed.
Generating the kinship matrix...OK

233 of in total 233 trait values can be matched to IDs in the pedigree.
Removing singletons... 8000 removed.
Removing singletons... none present.


RUNIT TEST PROTOCOL -- Wed Oct 16 02:47:34 2019 
*********************************************** 
Number of test functions: 59 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FamAgg RUnit Tests - 59 test functions, 0 errors, 0 failures
Number of test functions: 59 
Number of errors: 0 
Number of failures: 0 
There were 30 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 42.005   4.174  46.210 

name	user	system	elapsed
FABinTestResults	0.345	0.036	0.383
FAData-analysis	1.963	0.114	2.078
FAData	1.123	0.051	1.178
FAGenIndexResults	1.376	0.089	1.467
FAIncidenceRateResults	0.419	0.038	0.457
FAKinGroupResults	3.225	0.096	3.491
FAKinSumResults	1.889	0.044	1.941
FAStdIncidenceRateResults	0.524	0.034	0.567
Pedigree-utils	0.372	0.034	0.409
defineControls	0.194	0.024	0.219
plotting-functions	0.135	0.013	0.149