Stephanie M. Gogarten
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GENESIS |
| Branch: RELEASE_3_8 |
| Last Commit: 0b4d36e |
| Last Changed Date: 2019-02-20 14:45:04 -0400 (Wed, 20 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:25:04 -0400 (Sat, 13 Apr 2019).
| Package 609/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GENESIS 2.12.4 Stephanie M. Gogarten
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GENESIS |
| Version: 2.12.4 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENESIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GENESIS_2.12.4.tar.gz |
| StartedAt: 2019-04-13 02:30:45 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:42:23 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 697.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GENESIS.Rcheck |
| Warnings: NA |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GENESIS.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GENESIS_2.12.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GENESIS.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 'GENESIS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GENESIS' version '2.12.4'
* 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 'GENESIS' 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 ... NOTE
Unexported object imported by a ':::' call: 'survey:::saddle'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.pcrelate: no visible binding for global variable 'k'
calcISAFBeta: no visible binding for global variable 'k'
pcrelateSampBlock: no visible binding for global variable 'k'
Undefined global functions or variables:
k
* 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
varCompCI 13.78 0.61 14.35
pcrelate 13.29 0.61 13.90
fitNullModel 13.02 0.58 13.59
admixMap 9.21 0.50 9.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitNullModel 14.90 0.47 15.36
admixMap 13.19 0.62 13.82
varCompCI 10.85 0.41 11.25
pcrelate 10.62 0.42 11.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
[13] 0.383 - 0.383 == 0.000164
[31] 0.683 - 0.683 == 0.000174
[34] 0.800 - 0.800 == -0.000133
[51] 0.409 - 0.409 == -0.000145
[53] 0.692 - 0.692 == 0.000155
[55] 0.909 - 0.909 == -0.000138
[76] 0.733 - 0.733 == 0.000125
...
== testthat results ===========================================================
OK: 356 SKIPPED: 0 FAILED: 1
1. Failure: singleVarTest - logistic - score (@test_single_var_association_tests.R#89)
Error: testthat unit tests failed
Execution halted
** 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: 1 ERROR, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/GENESIS.Rcheck/00check.log'
for details.
GENESIS.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/GENESIS_2.12.4.tar.gz && rm -rf GENESIS.buildbin-libdir && mkdir GENESIS.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GENESIS.buildbin-libdir GENESIS_2.12.4.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GENESIS_2.12.4.zip && rm GENESIS_2.12.4.tar.gz GENESIS_2.12.4.zip
###
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100 2046k 100 2046k 0 0 34.4M 0 --:--:-- --:--:-- --:--:-- 36.3M
install for i386
* installing *source* package 'GENESIS' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GENESIS'
finding HTML links ... done
GENESIS-package html
HapMap_ASW_MXL_KINGmat html
admixMap html
finding level-2 HTML links ... done
admixMapMM html
assocTestAggregate html
assocTestMM html
assocTestSingle html
defunct html
deprecated html
fitNullMM html
fitNullModel html
fitNullReg html
kin2gds html
king2mat html
kingToMatrix html
makeSparseMatrix html
pcair html
pcairPartition html
pcrelate html
pcrelateMakeGRM html
pcrelateReadInbreed html
pcrelateReadKinship html
pcrelateToMatrix html
pcrelate_deprecated html
plot.pcair html
print.pcair html
sample_annotation_1KG html
varCompCI html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GENESIS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GENESIS' as GENESIS_2.12.4.zip
* DONE (GENESIS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GENESIS' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
GENESIS.Rcheck/tests_i386/testthat.Rout.fail
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.
> library(testthat)
> library(GENESIS)
>
> test_check("GENESIS")
-- 1. Failure: singleVarTest - logistic - score (@test_single_var_association_te
`res.glm` not equivalent to test.score$Score.pval.
34/200 mismatches (average diff: 0.000145)
[5] 0.890 - 0.890 == 0.000253
[10] 0.874 - 0.874 == 0.000119
[13] 0.383 - 0.383 == 0.000164
[31] 0.683 - 0.683 == 0.000174
[34] 0.800 - 0.800 == -0.000133
[51] 0.409 - 0.409 == -0.000145
[53] 0.692 - 0.692 == 0.000155
[55] 0.909 - 0.909 == -0.000138
[76] 0.733 - 0.733 == 0.000125
...
== testthat results ===========================================================
OK: 356 SKIPPED: 0 FAILED: 1
1. Failure: singleVarTest - logistic - score (@test_single_var_association_tests.R#89)
Error: testthat unit tests failed
Execution halted
|
GENESIS.Rcheck/tests_x64/testthat.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.
> library(testthat)
> library(GENESIS)
>
> test_check("GENESIS")
== testthat results ===========================================================
OK: 354 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
71.70 3.46 120.45
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GENESIS.Rcheck/examples_i386/GENESIS-Ex.timings
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GENESIS.Rcheck/examples_x64/GENESIS-Ex.timings
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