Johannes Rainer
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/FamAgg |
| Branch: RELEASE_3_8 |
| Last Commit: fba0bfc |
| Last Changed Date: 2019-03-26 03:37:29 -0400 (Tue, 26 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:07 -0400 (Sat, 13 Apr 2019).
| Package 504/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FamAgg 1.10.4 Johannes Rainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: FamAgg |
| Version: 1.10.4 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FamAgg.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FamAgg_1.10.4.tar.gz |
| StartedAt: 2019-04-13 02:11:14 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:14:45 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 211.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FamAgg.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FamAgg.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FamAgg_1.10.4.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/FamAgg.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'FamAgg/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'FamAgg' version '1.10.4' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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
FamAgg.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/FamAgg_1.10.4.tar.gz && rm -rf FamAgg.buildbin-libdir && mkdir FamAgg.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FamAgg.buildbin-libdir FamAgg_1.10.4.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL FamAgg_1.10.4.zip && rm FamAgg_1.10.4.tar.gz FamAgg_1.10.4.zip
###
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install for i386
* installing *source* package 'FamAgg' ...
** 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
converting help for package 'FamAgg'
finding HTML links ... done
FABinTestResults html
FAData-analysis html
FAData html
FAGenIndexResults html
FAIncidenceRateResults html
FAKinGroupResults html
FAKinSumResults html
FAProbResults html
FAStdIncidenceRateResults html
Pedigree-utils html
defineControls html
plotting-functions html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'FamAgg' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FamAgg' as FamAgg_1.10.4.zip
* DONE (FamAgg)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'FamAgg' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
FamAgg.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...OK
Generating the kinship matrix...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...OK
Generating the kinship matrix...OK
Generating the kinship matrix...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...OK
Generating the kinship matrix...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.ped.gz ...OK
Generating the kinship matrix...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/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 C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpgnKsUu\file244c5e5549bd.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 1.1-22
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 -- Sat Apr 13 02:14:08 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
31.06 2.34 34.01
|
FamAgg.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...OK
Generating the kinship matrix...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...OK
Generating the kinship matrix...OK
Generating the kinship matrix...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.txt ...OK
Generating the kinship matrix...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/library/FamAgg/txt/minnbreastsub.ped.gz ...OK
Generating the kinship matrix...OK
Reading pedigree information from file C:/Users/biocbuild/bbs-3.8-bioc/R/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 C:\Users\biocbuild\bbs-3.8-bioc\tmpdir\RtmpOM6Bdn\file1d7cc741041.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 1.1-22
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 -- Sat Apr 13 02:14:39 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
28.76 1.82 30.57
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FamAgg.Rcheck/examples_i386/FamAgg-Ex.timings
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FamAgg.Rcheck/examples_x64/FamAgg-Ex.timings
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