CHECK report for DEScan2 on merida1
This page was generated on 2021-05-06 12:34:47 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the DEScan2 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
|
| DEScan2 1.10.0 (landing page)
Dario Righelli
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/DEScan2 |
| Branch: RELEASE_3_12 |
| Last Commit: 7a7d1be |
| Last Changed Date: 2020-10-27 11:32:55 -0400 (Tue, 27 Oct 2020) |
| 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 | | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEScan2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEScan2_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/DEScan2.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEScan2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEScan2’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘DEScan2’ 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
* 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 ... 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 ... WARNING
Codoc mismatches from documentation object 'constructBedRanges':
constructBedRanges
Code: function(filename, filetype = c("bam", "bed", "bed.zip",
"narrow", "broad"), genomeName = NULL, onlyStdChrs =
FALSE, arePeaks = FALSE, verbose = FALSE)
Docs: function(filename, filetype = c("bam", "bed", "bed.zip"),
genomeName = NULL, onlyStdChrs = FALSE, arePeaks =
FALSE, verbose = FALSE)
Mismatches in argument default values:
Name: 'filetype' Code: c("bam", "bed", "bed.zip", "narrow", "broad") Docs: c("bam", "bed", "bed.zip")
Codoc mismatches from documentation object 'readFilesAsGRangesList':
readFilesAsGRangesList
Code: function(filePath, fileType = c("bam", "bed", "bed.zip",
"narrow", "broad"), genomeName = NULL, onlyStdChrs =
TRUE, arePeaks = TRUE, verbose = TRUE)
Docs: function(filePath, fileType = c("bam", "bed", "bed.zip"),
genomeName = NULL, onlyStdChrs = TRUE, arePeaks =
TRUE, verbose = TRUE)
Mismatches in argument default values:
Name: 'fileType' Code: c("bam", "bed", "bed.zip", "narrow", "broad") Docs: c("bam", "bed", "bed.zip")
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
findPeaks 27.502 1.369 29.121
finalRegions 28.519 0.279 28.838
findOverlapsOverSamples 14.843 0.032 14.892
binnedCoverage 12.602 0.442 13.304
countFinalRegions 5.528 0.426 5.969
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.12-bioc/meat/DEScan2.Rcheck/00check.log’
for details.
Installation output
DEScan2.Rcheck/00install.out
Tests output
DEScan2.Rcheck/tests/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-apple-darwin17.0 (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("DEScan2")
Loading required package: GenomicRanges
Loading required package: stats4
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
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
>
> test_check("DEScan2")
Maximizing with zthresh: 10 sigwin: 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
>
> proc.time()
user system elapsed
62.611 2.204 66.808
Example timings
DEScan2.Rcheck/DEScan2-Ex.timings