Thomas Sherman
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/RVS |
| Branch: RELEASE_3_12 |
| Last Commit: a28e783 |
| Last Changed Date: 2020-10-27 11:26:21 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:24 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the RVS package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1606/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RVS 1.12.0 (landing page) Thomas Sherman
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RVS |
| Version: 1.12.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RVS_1.12.0.tar.gz |
| StartedAt: 2021-05-06 06:33:31 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:40:09 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 397.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RVS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RVS_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RVS.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RVS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RVS' version '1.12.0'
* package encoding: UTF-8
* 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 whether package 'RVS' 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RVgene 13.78 1.45 16.79
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RVgene 14.08 0.5 16.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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
RVS.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/RVS_1.12.0.tar.gz && rm -rf RVS.buildbin-libdir && mkdir RVS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RVS.buildbin-libdir RVS_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RVS_1.12.0.zip && rm RVS_1.12.0.tar.gz RVS_1.12.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 755k 100 755k 0 0 13.1M 0 --:--:-- --:--:-- --:--:-- 13.4M
install for i386
* installing *source* package 'RVS' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RVS'
finding HTML links ... done
ComputeKinshipPropCoef-methods html
GeneDrop html
RVS html
RVgene html
RVsharing-methods html
SnpMatrixToCount html
ancestorDistance html
areMating html
checkArgs html
computePFU html
computePhiVec html
convertMatrix html
createNetwork html
denomProb html
enrichmentPValue html
enrichmentPValue_R_Backend html
ex.ped.mat html
exactSharingProb html
extract_carriers html
fam15157.vcf html
fam28003.vcf html
founderOccurence html
get.psubset html
inferNumAlleles html
inferTheta html
isDescendant html
marginalProb html
monteCarloSharingProb html
multipleFamilyPValue html
multipleFamilyPValue_R_Backend html
multipleVariantPValue html
multipleVariantPValue_R_Backend html
numerProb html
oldArgs html
oneFounderSharingProb html
oneFounderSharingProbSplitting html
ped2trio html
processPedigree-methods html
relatedFoundersCorrection html
runMonteCarlo html
samplePedigrees html
simulatePedigree html
snpMat html
twoFounderSharingProb html
** 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
install for x64
* installing *source* package 'RVS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RVS' as RVS_1.12.0.zip
* DONE (RVS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RVS' successfully unpacked and MD5 sums checked
|
RVS.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> library(testthat)
> library(RVS)
>
> test_check('RVS')
Founder 2 subped size 20
Founder 4 subped size 11
Founder 5 subped size 16
Founder 9 subped size 5
Founder 13 subped size 5
Founder 14 subped size 3
Founder 16 subped size 5
[1] 0.01873 0.49970 0.48150
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 113 ]
>
> proc.time()
user system elapsed
82.42 0.46 84.81
|
RVS.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> library(testthat)
> library(RVS)
>
> test_check('RVS')
Founder 2 subped size 20
Founder 4 subped size 11
Founder 5 subped size 16
Founder 9 subped size 5
Founder 13 subped size 5
Founder 14 subped size 3
Founder 16 subped size 5
[1] 0.01873 0.49970 0.48150
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 113 ]
>
> proc.time()
user system elapsed
133.60 0.45 134.06
|
|
RVS.Rcheck/examples_i386/RVS-Ex.timings
|
RVS.Rcheck/examples_x64/RVS-Ex.timings
|