Olivier Gevaert
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/MethylMix |
| git_branch: RELEASE_3_14 |
| git_last_commit: 6ec065d |
| git_last_commit_date: 2021-10-26 12:15:36 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:52 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the MethylMix package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MethylMix.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1123/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MethylMix 2.24.0 (landing page) Olivier Gevaert
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 2.24.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylMix.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MethylMix_2.24.0.tar.gz |
| StartedAt: 2022-04-12 22:41:24 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 22:46:11 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 286.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MethylMix.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylMix.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MethylMix_2.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MethylMix.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '2.24.0'
* 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 LazyData ... 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 30.50 0.16 30.65
MethylMix 26.58 0.06 26.64
MethylMix_Predict 26.17 0.08 26.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MethylMix_PlotModel 28.56 0.08 28.64
MethylMix_Predict 24.50 0.00 24.50
MethylMix 24.05 0.02 24.06
* 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-3.14-bioc/meat/MethylMix.Rcheck/00check.log'
for details.
MethylMix.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MethylMix_2.24.0.tar.gz && rm -rf MethylMix.buildbin-libdir && mkdir MethylMix.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethylMix.buildbin-libdir MethylMix_2.24.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MethylMix_2.24.0.zip && rm MethylMix_2.24.0.tar.gz MethylMix_2.24.0.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
24 2582k 24 643k 0 0 1428k 0 0:00:01 --:--:-- 0:00:01 1429k
100 2582k 100 2582k 0 0 2232k 0 0:00:01 0:00:01 --:--:-- 2234k
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_2.24.0.zip
* DONE (MethylMix)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MethylMix' successfully unpacked and MD5 sums checked
|
MethylMix.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
28.54 0.14 28.67
|
MethylMix.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
27.67 0.09 27.75
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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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