Weixin Cai
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/adaptest |
| Branch: master |
| Last Commit: 156e9d8 |
| Last Changed Date: 2018-10-30 11:54:39 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:37:32 -0400 (Tue, 09 Apr 2019).
| Package 17/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| adaptest 1.3.0 Weixin Cai
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: adaptest |
| Version: 1.3.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:adaptest.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings adaptest_1.3.0.tar.gz |
| StartedAt: 2019-04-09 01:00:23 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:12:48 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 745.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: adaptest.Rcheck |
| Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:adaptest.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings adaptest_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/adaptest.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'adaptest/DESCRIPTION' ... OK * this is package 'adaptest' version '1.3.0' * 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 'adaptest' 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 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' ERROR ** running tests for arch 'x64' ... Running 'testthat.R' ERROR * 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: 2 ERRORs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/adaptest.Rcheck/00check.log' for details.
adaptest.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/adaptest_1.3.0.tar.gz && rm -rf adaptest.buildbin-libdir && mkdir adaptest.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=adaptest.buildbin-libdir adaptest_1.3.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL adaptest_1.3.0.zip && rm adaptest_1.3.0.tar.gz adaptest_1.3.0.zip
###
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install for i386
* installing *source* package 'adaptest' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'adaptest'
finding HTML links ... done
adapTMLE-class html
adaptest html
adaptest_old html
bioadaptest html
cv_param_est html
data_adapt html
get_composition html
get_pval html
get_results_adaptmle html
get_significant_biomarker html
plot.data_adapt html
print.data_adapt html
rank_DE html
rank_ttest html
simulated_array html
simulated_treatment html
summary.data_adapt 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 'adaptest' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'adaptest' as adaptest_1.3.0.zip
* DONE (adaptest)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'adaptest' successfully unpacked and MD5 sums checked
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adaptest.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(adaptest)
adaptest v1.3.0: Data-Adaptive Statistics for High-Dimensional Multiple Testing
>
> Sys.setenv(R_TESTS = "")
> test_check("adaptest")
-- 1. Error: (unknown) (@test-old_vs_new.R#72) --------------------------------
error writing to connection
1: system.time(result_new <- adaptest(Y = Y, A = A.sample.vec, n_top = p.true + 5, n_fold = 4,
learning_library = c("SL.mean", "SL.glm", "SL.step"))) at testthat/test-old_vs_new.R:72
2: adaptest(Y = Y, A = A.sample.vec, n_top = p.true + 5, n_fold = 4, learning_library = c("SL.mean",
"SL.glm", "SL.step"))
3: origami::cross_validate(cv_fun = cv_param_est, folds = folds, data = df_all, parameter_wrapper = parameter_wrapper,
absolute = absolute, negative = negative, n_top = n_top, learning_library = learning_library,
Y_name = Y_name, A_name = A_name, W_name = W_name)
4: future.apply::future_lapply(folds, wrapped_fun, ...)
5: future({
...future.globals.maxSize.org <- getOption("future.globals.maxSize")
if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {
oopts <- options(future.globals.maxSize = ...future.globals.maxSize)
on.exit(options(oopts), add = TRUE)
}
lapply(seq_along(...future.elements_ii), FUN = function(jj) {
...future.X_jj <- ...future.elements_ii[[jj]]
...future.FUN(...future.X_jj, ...)
})
}, envir = envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii,
packages = packages_ii, lazy = future.lazy)
6: evaluator(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
packages = packages, ...)
7: fun(expr = expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
workers = workers, gc = gc, earlySignal = earlySignal, label = label, ...)
8: run(future)
9: run.ClusterFuture(future)
10: clusterCall(cl, fun = grmall)
11: sendCall(cl[[i]], fun, list(...))
12: postNode(con, "EXEC", list(fun = fun, args = args, return = return, tag = tag))
13: sendData(con, list(type = type, data = value, tag = tag))
14: sendData.SOCKnode(con, list(type = type, data = value, tag = tag))
15: serialize(data, node$con)
== testthat results ===========================================================
OK: 1 SKIPPED: 1 FAILED: 1
1. Error: (unknown) (@test-old_vs_new.R#72)
Error: testthat unit tests failed
Execution halted
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adaptest.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(adaptest)
adaptest v1.3.0: Data-Adaptive Statistics for High-Dimensional Multiple Testing
>
> Sys.setenv(R_TESTS = "")
> test_check("adaptest")
-- 1. Error: (unknown) (@test-old_vs_new.R#72) --------------------------------
error writing to connection
1: system.time(result_new <- adaptest(Y = Y, A = A.sample.vec, n_top = p.true + 5, n_fold = 4,
learning_library = c("SL.mean", "SL.glm", "SL.step"))) at testthat/test-old_vs_new.R:72
2: adaptest(Y = Y, A = A.sample.vec, n_top = p.true + 5, n_fold = 4, learning_library = c("SL.mean",
"SL.glm", "SL.step"))
3: origami::cross_validate(cv_fun = cv_param_est, folds = folds, data = df_all, parameter_wrapper = parameter_wrapper,
absolute = absolute, negative = negative, n_top = n_top, learning_library = learning_library,
Y_name = Y_name, A_name = A_name, W_name = W_name)
4: future.apply::future_lapply(folds, wrapped_fun, ...)
5: future({
...future.globals.maxSize.org <- getOption("future.globals.maxSize")
if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) {
oopts <- options(future.globals.maxSize = ...future.globals.maxSize)
on.exit(options(oopts), add = TRUE)
}
lapply(seq_along(...future.elements_ii), FUN = function(jj) {
...future.X_jj <- ...future.elements_ii[[jj]]
...future.FUN(...future.X_jj, ...)
})
}, envir = envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii,
packages = packages_ii, lazy = future.lazy)
6: evaluator(expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
packages = packages, ...)
7: fun(expr = expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals,
workers = workers, gc = gc, earlySignal = earlySignal, label = label, ...)
8: run(future)
9: run.ClusterFuture(future)
10: clusterCall(cl, fun = grmall)
11: sendCall(cl[[i]], fun, list(...))
12: postNode(con, "EXEC", list(fun = fun, args = args, return = return, tag = tag))
13: sendData(con, list(type = type, data = value, tag = tag))
14: sendData.SOCKnode(con, list(type = type, data = value, tag = tag))
15: serialize(data, node$con)
== testthat results ===========================================================
OK: 1 SKIPPED: 1 FAILED: 1
1. Error: (unknown) (@test-old_vs_new.R#72)
Error: testthat unit tests failed
Execution halted
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adaptest.Rcheck/examples_i386/adaptest-Ex.timings
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adaptest.Rcheck/examples_x64/adaptest-Ex.timings
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