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CHECK report for mCSEA on tokay1

This page was generated on 2019-04-13 11:28:44 -0400 (Sat, 13 Apr 2019).

Package 898/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mCSEA 1.2.2
Jordi Martorell-Marugán
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/mCSEA
Branch: RELEASE_3_8
Last Commit: 5c1c44d
Last Changed Date: 2019-02-13 06:10:56 -0400 (Wed, 13 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mCSEA
Version: 1.2.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mCSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mCSEA_1.2.2.tar.gz
StartedAt: 2019-04-13 03:35:01 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:42:49 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 467.2 seconds
RetCode: 0
Status:  OK  
CheckDir: mCSEA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mCSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mCSEA_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/mCSEA.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 'mCSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mCSEA' version '1.2.2'
* package encoding: UTF-8
* 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 'mCSEA' 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
Examples with CPU or elapsed time > 5s
                user system elapsed
mCSEAPlot      10.44   0.73   14.73
mCSEAIntegrate  5.04   0.49   16.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mCSEAPlot      10.88   0.26   13.76
mCSEAIntegrate  5.03   0.35   18.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: OK

Installation output

mCSEA.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/mCSEA_1.2.2.tar.gz && rm -rf mCSEA.buildbin-libdir && mkdir mCSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mCSEA.buildbin-libdir mCSEA_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL mCSEA_1.2.2.zip && rm mCSEA_1.2.2.tar.gz mCSEA_1.2.2.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 1547k  100 1547k    0     0  26.1M      0 --:--:-- --:--:-- --:--:-- 27.9M

install for i386

* installing *source* package 'mCSEA' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mCSEA'
    finding HTML links ... done
    exprTest                                html  
    mCSEA-package                           html  
    mCSEAIntegrate                          html  
    mCSEAPlot                               html  
    mCSEAPlotGSEA                           html  
    mCSEATest                               html  
    precomputedmCSEA                        html  
    rankProbes                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'mCSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mCSEA' as mCSEA_1.2.2.zip
* DONE (mCSEA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'mCSEA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

mCSEA.Rcheck/tests_i386/runTests.Rout


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.

> BiocGenerics:::testPackage("mCSEA")

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows




Attaching package: 'mCSEA'

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

    exprTest

Integrating promoters methylation with gene expression
Associating CpG sites to promoters
Analysing promoters
0 DMRs found (padj < 0.05)
Transforming beta-values to M-values
Calculating linear model...
	Explanatory variable: expla
	Case group: Case
	Reference group: Control
	Total samples: 20
	Covariates: None
	Categorical variables: expla cov1
	Continuous variables: None


RUNIT TEST PROTOCOL -- Sat Apr 13 03:42:00 2019 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mCSEA RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In fgsea::fgsea(genes, rank, minSize = minCpGs, nperm = nperm, nproc = nproc) :
  There are ties in the preranked stats (15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
2: In fgsea::fgsea(genes, rank, minSize = minCpGs, nperm = nperm, nproc = nproc) :
  There are duplicate gene names, fgsea may produce unexpected results
> 
> proc.time()
   user  system elapsed 
  19.34    1.51   36.09

mCSEA.Rcheck/tests_x64/runTests.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.

> BiocGenerics:::testPackage("mCSEA")

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows




Attaching package: 'mCSEA'

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

    exprTest

Integrating promoters methylation with gene expression
Associating CpG sites to promoters
Analysing promoters
0 DMRs found (padj < 0.05)
Transforming beta-values to M-values
Calculating linear model...
	Explanatory variable: expla
	Case group: Case
	Reference group: Control
	Total samples: 20
	Covariates: None
	Categorical variables: expla cov1
	Continuous variables: None


RUNIT TEST PROTOCOL -- Sat Apr 13 03:42:44 2019 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mCSEA RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In fgsea::fgsea(genes, rank, minSize = minCpGs, nperm = nperm, nproc = nproc) :
  There are ties in the preranked stats (15% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
2: In fgsea::fgsea(genes, rank, minSize = minCpGs, nperm = nperm, nproc = nproc) :
  There are duplicate gene names, fgsea may produce unexpected results
> 
> proc.time()
   user  system elapsed 
   25.4     1.1    42.9

Example timings

mCSEA.Rcheck/examples_i386/mCSEA-Ex.timings

nameusersystemelapsed
mCSEA-package0.080.000.08
mCSEAIntegrate 5.04 0.4916.84
mCSEAPlot10.44 0.7314.73
mCSEAPlotGSEA0.310.050.36
mCSEATest0.050.000.05
rankProbes0.250.030.28

mCSEA.Rcheck/examples_x64/mCSEA-Ex.timings

nameusersystemelapsed
mCSEA-package0.030.030.06
mCSEAIntegrate 5.03 0.3518.31
mCSEAPlot10.88 0.2613.76
mCSEAPlotGSEA0.310.030.35
mCSEATest0.030.020.04
rankProbes0.250.010.27