Thomas Sherman
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/RVS |
| Branch: RELEASE_3_9 |
| Last Commit: fde2fb2 |
| Last Changed Date: 2019-05-02 11:54:07 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:39:02 -0400 (Wed, 16 Oct 2019).
| Package 1443/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RVS 1.6.0 Thomas Sherman
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RVS |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RVS_1.6.0.tar.gz |
| StartedAt: 2019-10-16 06:51:29 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:57:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 335.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RVS.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RVS.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RVS_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RVS.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.6.0'
* 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 or elapsed time > 5s
user system elapsed
RVgene 12.36 0.94 13.34
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RVgene 11.85 0.31 12.58
* 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
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RVS_1.6.0.tar.gz && rm -rf RVS.buildbin-libdir && mkdir RVS.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RVS.buildbin-libdir RVS_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RVS_1.6.0.zip && rm RVS_1.6.0.tar.gz RVS_1.6.0.zip
###
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% 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 752k 100 752k 0 0 11.3M 0 --:--:-- --:--:-- --:--:-- 12.6M
install for i386
* installing *source* package 'RVS' ...
** using staged installation
** R
** data
** 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
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
multipleVariantPValue 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_1.6.0.zip
* DONE (RVS)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RVS' successfully unpacked and MD5 sums checked
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RVS.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> 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
== testthat results ===========================================================
[ OK: 111 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
76.18 0.54 81.43
|
RVS.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> 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
== testthat results ===========================================================
[ OK: 111 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
95.34 0.40 95.78
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RVS.Rcheck/examples_i386/RVS-Ex.timings
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RVS.Rcheck/examples_x64/RVS-Ex.timings
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