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CHECK report for adaptest on tokay2

This page was generated on 2019-04-09 12:37:32 -0400 (Tue, 09 Apr 2019).

Package 17/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adaptest 1.3.0
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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 UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

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

Command output

##############################################################################
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###
### 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
###
##############################################################################
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* 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.


Installation output

adaptest.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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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  % 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  824k  100  824k    0     0  8455k      0 --:--:-- --:--:-- --:--:-- 9063k

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

Tests output

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

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

Example timings

adaptest.Rcheck/examples_i386/adaptest-Ex.timings

nameusersystemelapsed
adapTMLE-class2.500.302.79
adaptest3.570.343.94
bioadaptest3.610.053.66
get_composition4.410.004.41
get_significant_biomarker3.900.063.97
rank_DE0.830.050.87
rank_ttest0.220.090.32

adaptest.Rcheck/examples_x64/adaptest-Ex.timings

nameusersystemelapsed
adapTMLE-class2.800.102.91
adaptest4.680.084.76
bioadaptest2.660.142.80
get_composition3.770.003.76
get_significant_biomarker4.260.024.28
rank_DE0.890.030.92
rank_ttest0.240.000.24