Olivier Gevaert
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/MethylMix |
| Branch: RELEASE_3_11 |
| Last Commit: 8d6e047 |
| Last Changed Date: 2020-04-27 14:42:42 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:04 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE MethylMix PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1061/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MethylMix 2.18.0 Olivier Gevaert
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: MethylMix |
| Version: 2.18.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylMix.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MethylMix_2.18.0.tar.gz |
| StartedAt: 2020-10-17 05:57:54 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:03:00 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 306.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethylMix.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylMix.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MethylMix_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MethylMix.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 'MethylMix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylMix' version '2.18.0'
* 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 ... NOTE
MethylMix: no visible global function definition for 'is'
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 (user + system) or elapsed time > 5s
user system elapsed
MethylMix_PlotModel 30.67 0.14 30.82
MethylMix_Predict 26.74 0.08 26.81
MethylMix 25.25 0.05 25.30
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MethylMix_PlotModel 33.02 0.10 33.11
MethylMix_Predict 31.42 0.06 31.50
MethylMix 29.61 0.04 29.66
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/MethylMix.Rcheck/00check.log'
for details.
MethylMix.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MethylMix_2.18.0.tar.gz && rm -rf MethylMix.buildbin-libdir && mkdir MethylMix.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethylMix.buildbin-libdir MethylMix_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MethylMix_2.18.0.zip && rm MethylMix_2.18.0.tar.gz MethylMix_2.18.0.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 2585k 100 2585k 0 0 25.4M 0 --:--:-- --:--:-- --:--:-- 27.1M
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_2.18.0.zip
* DONE (MethylMix)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MethylMix' successfully unpacked and MD5 sums checked
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MethylMix.Rcheck/tests_i386/testthat.Rout
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(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
30.71 0.18 30.89
|
MethylMix.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(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
34.70 0.14 34.82
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MethylMix.Rcheck/examples_i386/MethylMix-Ex.timings
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MethylMix.Rcheck/examples_x64/MethylMix-Ex.timings
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