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CHECK report for MethylMix on tokay2

This page was generated on 2019-10-16 12:30:55 -0400 (Wed, 16 Oct 2019).

Package 982/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MethylMix 2.14.0
Olivier Gevaert
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MethylMix
Branch: RELEASE_3_9
Last Commit: 3cde4ad
Last Changed Date: 2019-05-02 11:53:49 -0400 (Thu, 02 May 2019)
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 [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MethylMix
Version: 2.14.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylMix.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MethylMix_2.14.0.tar.gz
StartedAt: 2019-10-16 05:09:27 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:14:49 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 322.1 seconds
RetCode: 0
Status:  OK  
CheckDir: MethylMix.Rcheck
Warnings: 0

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:MethylMix.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MethylMix_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MethylMix.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethylMix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylMix' version '2.14.0'
* 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 'MethylMix' 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 ... NOTE
Namespace in Imports field not imported from: 'digest'
  All declared Imports should be used.
* 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
MethylMix_PlotModel 37.27   0.02   37.29
MethylMix_Predict   34.62   0.02   34.64
MethylMix           32.83   0.06   33.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
MethylMix_PlotModel 32.87   0.02   32.89
MethylMix           29.75   0.01   29.77
MethylMix_Predict   28.38   0.01   28.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/MethylMix.Rcheck/00check.log'
for details.



Installation output

MethylMix.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/MethylMix_2.14.0.tar.gz && rm -rf MethylMix.buildbin-libdir && mkdir MethylMix.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethylMix.buildbin-libdir MethylMix_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MethylMix_2.14.0.zip && rm MethylMix_2.14.0.tar.gz MethylMix_2.14.0.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 2583k  100 2583k    0     0   9.9M      0 --:--:-- --:--:-- --:--:-- 10.2M

install for i386

* installing *source* package 'MethylMix' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MethylMix'
    finding HTML links ... done
    BatchData                               html  
    ClusterProbes                           html  
    ComBat_NoFiles                          html  
    Download_DNAmethylation                 html  
    Download_GeneExpression                 html  
    GEcancer                                html  
    GetData                                 html  
    METcancer                               html  
    METnormal                               html  
    MethylMix                               html  
    MethylMix_MixtureModel                  html  
    MethylMix_ModelGeneExpression           html  
    MethylMix_ModelSingleGene               html  
    MethylMix_PlotModel                     html  
    MethylMix_Predict                       html  
    MethylMix_RemoveFlipOver                html  
    Preprocess_CancerSite_Methylation27k    html  
    Preprocess_CancerSite_Methylation450k   html  
    Preprocess_DNAmethylation               html  
    Preprocess_GeneExpression               html  
    Preprocess_MAdata_Cancer                html  
    Preprocess_MAdata_Normal                html  
    ProbeAnnotation                         html  
    SNPprobes                               html  
    TCGA_BatchCorrection_MolecularData      html  
    TCGA_GENERIC_BatchCorrection            html  
    TCGA_GENERIC_CheckBatchEffect           html  
    TCGA_GENERIC_CleanUpSampleNames         html  
    TCGA_GENERIC_GetSampleGroups            html  
    TCGA_GENERIC_LoadIlluminaMethylationData
                                            html  
    TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust
                                            html  
    TCGA_GENERIC_MergeData                  html  
    TCGA_Load_MolecularData                 html  
    TCGA_Process_EstimateMissingValues      html  
    betaEst_2                               html  
    blc_2                                   html  
    combineForEachOutput                    html  
    get_firehoseData                        html  
    predictOneGene                          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 'MethylMix' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethylMix' as MethylMix_2.14.0.zip
* DONE (MethylMix)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MethylMix' successfully unpacked and MD5 sums checked

Tests output

MethylMix.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(MethylMix)
> 
> test_check("MethylMix")
Found 251 samples with both methylation and expression data.
Correlating methylation data with gene expression...

Found 9 transcriptionally predictive genes.

Starting Beta mixture modeling.
Running Beta mixture model on 9 genes and on 251 samples.
ERBB2 :  2  components are best.
FAAH :  2  components are best.
FOXD1 :  2  components are best.
ME1 :  2  components are best.
MGMT :  2  components are best.
OAS1 :  2  components are best.
SOX10 :  2  components are best.
TRAF6 :  2  components are best.
ZNF217 :  2  components are best.
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  34.10    0.09   34.23 

MethylMix.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(MethylMix)
> 
> test_check("MethylMix")
Found 251 samples with both methylation and expression data.
Correlating methylation data with gene expression...

Found 9 transcriptionally predictive genes.

Starting Beta mixture modeling.
Running Beta mixture model on 9 genes and on 251 samples.
ERBB2 :  2  components are best.
FAAH :  2  components are best.
FOXD1 :  2  components are best.
ME1 :  2  components are best.
MGMT :  2  components are best.
OAS1 :  2  components are best.
SOX10 :  2  components are best.
TRAF6 :  2  components are best.
ZNF217 :  2  components are best.
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  31.04    0.12   31.14 

Example timings

MethylMix.Rcheck/examples_i386/MethylMix-Ex.timings

nameusersystemelapsed
ClusterProbes000
Download_DNAmethylation000
Download_GeneExpression000
GetData000
MethylMix32.83 0.0633.03
MethylMix_ModelGeneExpression0.030.010.05
MethylMix_PlotModel37.27 0.0237.29
MethylMix_Predict34.62 0.0234.64
Preprocess_DNAmethylation000
Preprocess_GeneExpression000

MethylMix.Rcheck/examples_x64/MethylMix-Ex.timings

nameusersystemelapsed
ClusterProbes000
Download_DNAmethylation000
Download_GeneExpression000
GetData000
MethylMix29.75 0.0129.77
MethylMix_ModelGeneExpression0.080.000.08
MethylMix_PlotModel32.87 0.0232.89
MethylMix_Predict28.38 0.0128.39
Preprocess_DNAmethylation000
Preprocess_GeneExpression000