Xavier Escribà Montagut
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/MEAL |
| Branch: RELEASE_3_12 |
| Last Commit: f173c88 |
| Last Changed Date: 2021-05-03 04:23:24 -0400 (Mon, 03 May 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:09 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the MEAL package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1028/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MEAL 1.20.4 (landing page) Xavier Escribà Montagut
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MEAL |
| Version: 1.20.4 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MEAL_1.20.4.tar.gz |
| StartedAt: 2021-05-06 04:20:56 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:30:11 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 554.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MEAL.Rcheck |
| Warnings: 5 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MEAL_1.20.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MEAL.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEAL/DESCRIPTION' ... OK
* this is package 'MEAL' version '1.20.4'
* 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 'MEAL' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpKC0lpg/R.INSTALL2d542e2a4cad/MEAL/man/runRDA.Rd:55: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MEAL.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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
plotRegion: no visible global function definition for
'subsetByOverlaps'
plotRegion: no visible global function definition for 'mcols<-'
runRDA: no visible global function definition for 'rowData'
runSVA: no visible global function definition for 'resid'
Undefined global functions or variables:
mcols<- resid rowData subsetByOverlaps
Consider adding
importFrom("stats", "resid")
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 ... WARNING
Codoc mismatches from documentation object 'getProbeResults':
getProbeResults
Code: function(object, rid = "DiffMean", coef = 2, contrast = NULL,
fNames = c("chromosome", "start"), robust = FALSE,
...)
Docs: function(object, rid = "DiffMean", coef = 2, contrast = NULL,
fNames = c("chromosome", "start"), ...)
Argument names in code not in docs:
robust
Mismatches in argument names:
Position: 6 Code: robust Docs: ...
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'runDiffMeanAnalysis'
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
Warning: 'runRegionAnalysis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
exportResults 8.27 0.54 11.15
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
Warning: 'runRegionAnalysis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
exportResults 6.86 0.26 7.13
* 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: 5 WARNINGs, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/MEAL.Rcheck/00check.log'
for details.
MEAL.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MEAL_1.20.4.tar.gz && rm -rf MEAL.buildbin-libdir && mkdir MEAL.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MEAL.buildbin-libdir MEAL_1.20.4.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MEAL_1.20.4.zip && rm MEAL_1.20.4.tar.gz MEAL_1.20.4.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 588k 100 588k 0 0 16.4M 0 --:--:-- --:--:-- --:--:-- 16.9M
install for i386
* installing *source* package 'MEAL' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MEAL'
finding HTML links ... done
MEAL-defunct html
MEAL html
computeRDAR2 html
correlationMethExprs html
exportResults html
filterResults html
getGeneVals html
getProbeResults html
getRDAresults html
plotFeature html
plotRDA html
plotRegion html
runBlockFinder html
runBumphunter html
runDMRcate html
runDiffMeanAnalysis html
runDiffVarAnalysis html
runPipeline html
runRDA html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpKC0lpg/R.INSTALL2d542e2a4cad/MEAL/man/runRDA.Rd:55: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
runRegionAnalysis html
topRDAhits 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 'MEAL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEAL' as MEAL_1.20.4.zip
* DONE (MEAL)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MEAL' successfully unpacked and MD5 sums checked
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MEAL.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(MEAL)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
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.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: MultiDataSet
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("MEAL")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
37.78 4.43 43.90
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MEAL.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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(MEAL)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
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.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: MultiDataSet
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
>
> test_check("MEAL")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]
>
> proc.time()
user system elapsed
36.43 1.92 39.92
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MEAL.Rcheck/examples_i386/MEAL-Ex.timings
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MEAL.Rcheck/examples_x64/MEAL-Ex.timings
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