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CHECK report for methylCC on tokay2

This page was generated on 2020-10-17 11:57:04 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE methylCC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1057/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylCC 1.2.0
Stephanie C. Hicks
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/methylCC
Branch: RELEASE_3_11
Last Commit: 8258eb6
Last Changed Date: 2020-04-27 15:31:08 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylCC
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylCC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methylCC_1.2.0.tar.gz
StartedAt: 2020-10-17 05:57:26 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:10:51 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 804.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: methylCC.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylCC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings methylCC_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/methylCC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylCC/DESCRIPTION' ... OK
* this is package 'methylCC' version '1.2.0'
* 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 'methylCC' 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 the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    1. methylCC::estimatecc(object = FlowSorted.Blood.450k.sub)
    4. methylCC:::.find_dmrs(...)
    6. minfi::getBeta(mset_train_flow_sort, type = "Illumina")
    7. minfi:::.local(object, ...)
    8. minfi:::.betaFromMethUnmeth(...)
   10. DelayedArray::pmax2(Meth, 0)
   11. BiocGenerics::pmax(e1, e2)
   16. base::pmax(...)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: checking estimatecc output (without .find_dmrs) (@test-estimatecc.R#12) 
  
  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
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/methylCC.Rcheck/00check.log'
for details.


Installation output

methylCC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/methylCC_1.2.0.tar.gz && rm -rf methylCC.buildbin-libdir && mkdir methylCC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylCC.buildbin-libdir methylCC_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL methylCC_1.2.0.zip && rm methylCC_1.2.0.tar.gz methylCC_1.2.0.zip
###
##############################################################################
##############################################################################


  % 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 4170k  100 4170k    0     0  12.1M      0 --:--:-- --:--:-- --:--:-- 12.4M

install for i386

* installing *source* package 'methylCC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methylCC'
    finding HTML links ... done
    FlowSorted.Blood.450k.sub               html  
    cell_counts                             html  
    dot-WFun                                html  
    dot-extract_raw_data                    html  
    dot-find_dmrs                           html  
    dot-initializeMLEs                      html  
    dot-initialize_theta                    html  
    dot-methylcc_engine                     html  
    dot-methylcc_estep                      html  
    dot-methylcc_mstep                      html  
    dot-pick_target_positions               html  
    dot-preprocess_estimatecc               html  
    dot-splitit                             html  
    estimatecc-class                        html  
    estimatecc                              html  
    offMethRegions                          html  
    onMethRegions                           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 'methylCC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylCC' as methylCC_1.2.0.zip
* DONE (methylCC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'methylCC' successfully unpacked and MD5 sums checked

Tests output

methylCC.Rcheck/tests_i386/testthat.Rout.fail


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(methylCC)
Loading required package: FlowSorted.Blood.450k
Loading required package: minfi
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("methylCC")
-- 1. Error: checking estimatecc output (without .find_dmrs) (@test-estimatecc.R
cannot allocate vector of size 129.6 Mb
Backtrace:
  1. methylCC::estimatecc(object = FlowSorted.Blood.450k.sub)
  4. methylCC:::.find_dmrs(...)
  6. minfi::getBeta(mset_train_flow_sort, type = "Illumina")
  7. minfi:::.local(object, ...)
  8. minfi:::.betaFromMethUnmeth(...)
 10. DelayedArray::pmax2(Meth, 0)
 11. BiocGenerics::pmax(e1, e2)
 16. base::pmax(...)

== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Error: checking estimatecc output (without .find_dmrs) (@test-estimatecc.R#12) 

Error: testthat unit tests failed
Execution halted

methylCC.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(methylCC)
Loading required package: FlowSorted.Blood.450k
Loading required package: minfi
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("methylCC")
== testthat results  ===========================================================
[ OK: 1 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  98.71   18.21  120.07 

Example timings

methylCC.Rcheck/examples_i386/methylCC-Ex.timings

nameusersystemelapsed
cell_counts0.820.050.87
estimatecc-class0.830.000.83
estimatecc0.860.000.86

methylCC.Rcheck/examples_x64/methylCC-Ex.timings

nameusersystemelapsed
cell_counts0.920.040.96
estimatecc-class0.750.020.77
estimatecc1.080.021.09