Package: methyvim

Version: 1.5.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methyvim.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methyvim_1.5.0.tar.gz

StartedAt: 2019-04-09 04:12:00 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:39:49 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 1669.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: methyvim.Rcheck

Warnings: NA

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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:methyvim.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings methyvim_1.5.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/methyvim.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 'methyvim/DESCRIPTION' ... OK
* this is package 'methyvim' version '1.5.0'
* 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 'methyvim' 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
methyheat      10.62   0.93   11.75
plot.methytmle  7.56   0.14    7.71
methyvolc       7.11   0.25    7.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
methyheat      11.17   0.20   11.38
methyvolc       6.99   0.05    7.03
plot.methytmle  6.86   0.12    6.99
* 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:
  7: run(future)
  8: run.ClusterFuture(future)
  9: clusterCall(cl, fun = grmall)
  10: sendCall(cl[[i]], fun, list(...))
  11: postNode(con, "EXEC", list(fun = fun, args = args, return = return, tag = tag))
  12: sendData(con, list(type = type, data = value, tag = tag))
  13: sendData.SOCKnode(con, list(type = type, data = value, tag = tag))
  14: serialize(data, node$con)
  
  == testthat results  ===========================================================
  OK: 48 SKIPPED: 1 FAILED: 1
  1. Error: registers BiocParallel::DoparParam by default for parallel=TRUE (@test-set_parallel.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  7: run(future)
  8: run.ClusterFuture(future)
  9: clusterCall(cl, fun = grmall)
  10: sendCall(cl[[i]], fun, list(...))
  11: postNode(con, "EXEC", list(fun = fun, args = args, return = return, tag = tag))
  12: sendData(con, list(type = type, data = value, tag = tag))
  13: sendData.SOCKnode(con, list(type = type, data = value, tag = tag))
  14: serialize(data, node$con)
  
  == testthat results  ===========================================================
  OK: 48 SKIPPED: 1 FAILED: 1
  1. Error: registers future::multiprocess by default for parallel=TRUE (@test-set_parallel.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
* 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/methyvim.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/methyvim_1.5.0.tar.gz && rm -rf methyvim.buildbin-libdir && mkdir methyvim.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methyvim.buildbin-libdir methyvim_1.5.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL methyvim_1.5.0.zip && rm methyvim_1.5.0.tar.gz methyvim_1.5.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

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100  864k  100  864k    0     0  11.7M      0 --:--:-- --:--:-- --:--:-- 12.9M

install for i386

* installing *source* package 'methyvim' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methyvim'
    finding HTML links ... done
    cluster_sites                           html  
    fdr_msa                                 html  
    force_positivity                        html  
    limma_screen                            html  
    methyheat                               html  
    methytmle-class                         html  
    methyvim                                html  
    methyvim_tmle                           html  
    methyvolc                               html  
    plot.methytmle                          html  
    set_parallel                            html  
    wrap_in_try                             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 'methyvim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methyvim' as methyvim_1.5.0.zip
* DONE (methyvim)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'methyvim' successfully unpacked and MD5 sums checked

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(methyvim)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
methyvim v1.5.0: Targeted, Robust, and Model-free Differential Methylation Analysis
> 
> set.seed(43719)
> test_check("methyvim")
-- 1. Error: registers BiocParallel::DoparParam by default for parallel=TRUE (@t
error writing to connection
1: set_parallel(parallel = TRUE) at testthat/test-set_parallel.R:9
2: future::plan(future::multiprocess)
3: plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4: plan_init()
5: evaluator(NA, label = "future-plan-test", globals = FALSE, lazy = FALSE)
6: fun(expr = expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals, 
       workers = workers, gc = gc, earlySignal = earlySignal, label = label, ...)
7: run(future)
8: run.ClusterFuture(future)
9: clusterCall(cl, fun = grmall)
10: sendCall(cl[[i]], fun, list(...))
11: postNode(con, "EXEC", list(fun = fun, args = args, return = return, tag = tag))
12: sendData(con, list(type = type, data = value, tag = tag))
13: sendData.SOCKnode(con, list(type = type, data = value, tag = tag))
14: serialize(data, node$con)

== testthat results  ===========================================================
OK: 48 SKIPPED: 1 FAILED: 1
1. Error: registers BiocParallel::DoparParam by default for parallel=TRUE (@test-set_parallel.R#9) 

Error: testthat unit tests failed
Execution halted

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(methyvim)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
methyvim v1.5.0: Targeted, Robust, and Model-free Differential Methylation Analysis
> 
> set.seed(43719)
> test_check("methyvim")
-- 1. Error: registers future::multiprocess by default for parallel=TRUE (@test-
error writing to connection
1: set_parallel(parallel = TRUE) at testthat/test-set_parallel.R:14
2: future::plan(future::multiprocess)
3: plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
4: plan_init()
5: evaluator(NA, label = "future-plan-test", globals = FALSE, lazy = FALSE)
6: fun(expr = expr, envir = envir, substitute = FALSE, lazy = lazy, seed = seed, globals = globals, 
       workers = workers, gc = gc, earlySignal = earlySignal, label = label, ...)
7: run(future)
8: run.ClusterFuture(future)
9: clusterCall(cl, fun = grmall)
10: sendCall(cl[[i]], fun, list(...))
11: postNode(con, "EXEC", list(fun = fun, args = args, return = return, tag = tag))
12: sendData(con, list(type = type, data = value, tag = tag))
13: sendData.SOCKnode(con, list(type = type, data = value, tag = tag))
14: serialize(data, node$con)

== testthat results  ===========================================================
OK: 48 SKIPPED: 1 FAILED: 1
1. Error: registers future::multiprocess by default for parallel=TRUE (@test-set_parallel.R#14) 

Error: testthat unit tests failed
Execution halted