Jordi Martorell-Marugán
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/mCSEA |
| Branch: RELEASE_3_10 |
| Last Commit: a12fee2 |
| Last Changed Date: 2019-10-29 13:10:56 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:29:43 -0400 (Wed, 15 Apr 2020).
| Package 976/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mCSEA 1.6.0 Jordi Martorell-Marugán
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: mCSEA |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mCSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings mCSEA_1.6.0.tar.gz |
| StartedAt: 2020-04-15 04:31:19 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:39:04 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 465.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: mCSEA.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mCSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings mCSEA_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/mCSEA.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.0'
* 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 '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 ... NOTE
mCSEAIntegrate: no visible binding for global variable 'sd'
Undefined global functions or variables:
sd
Consider adding
importFrom("stats", "sd")
to your NAMESPACE file.
* 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 12.86 0.63 15.55
mCSEAIntegrate 5.34 0.37 24.21
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mCSEAPlot 13.45 0.25 14.83
mCSEAIntegrate 7.41 0.42 27.58
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/mCSEA.Rcheck/00check.log'
for details.
mCSEA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/mCSEA_1.6.0.tar.gz && rm -rf mCSEA.buildbin-libdir && mkdir mCSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mCSEA.buildbin-libdir mCSEA_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL mCSEA_1.6.0.zip && rm mCSEA_1.6.0.tar.gz mCSEA_1.6.0.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 1547k 100 1547k 0 0 9961k 0 --:--:-- --:--:-- --:--:-- 10.0M
install for i386
* installing *source* package 'mCSEA' ...
** using staged installation
** 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 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 'mCSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mCSEA' as mCSEA_1.6.0.zip
* DONE (mCSEA)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'mCSEA' successfully unpacked and MD5 sums checked
|
mCSEA.Rcheck/tests_i386/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.
> 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, 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
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
0 genes removed from exprData due to Standar Deviation = 0
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 -- Wed Apr 15 04:38:16 2020
***********************************************
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
17.32 1.75 32.95
|
mCSEA.Rcheck/tests_x64/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.
> 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, 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
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
0 genes removed from exprData due to Standar Deviation = 0
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 -- Wed Apr 15 04:39:00 2020
***********************************************
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
24.29 1.17 42.93
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mCSEA.Rcheck/examples_i386/mCSEA-Ex.timings
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mCSEA.Rcheck/examples_x64/mCSEA-Ex.timings
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