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This page was generated on 2024-04-17 11:37:45 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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

Package 776/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDNAx 1.0.2  (landing page)
Beatriz Calvo-Serra
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/gDNAx
git_branch: RELEASE_3_18
git_last_commit: 0fb2969
git_last_commit_date: 2024-03-15 15:38:59 -0400 (Fri, 15 Mar 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for gDNAx on merida1


To the developers/maintainers of the gDNAx package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gDNAx.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gDNAx
Version: 1.0.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDNAx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDNAx_1.0.2.tar.gz
StartedAt: 2024-04-16 03:03:32 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 03:24:17 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 1244.8 seconds
RetCode: 0
Status:   OK  
CheckDir: gDNAx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDNAx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDNAx_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/gDNAx.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDNAx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDNAx’ version ‘1.0.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gDNAx’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicAlignments:::.make_GAlignmentPairs_from_GAlignments’
  ‘GenomicAlignments:::.normargParam’ ‘S4Vectors:::makePowersOfTwo’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
filterBAMtx  141.497 11.642 195.774
gDNAdx       125.468  6.441 147.100
strandedness  58.529  3.174  74.041
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/gDNAx.Rcheck/00check.log’
for details.



Installation output

gDNAx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDNAx
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘gDNAx’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (gDNAx)

Tests output

gDNAx.Rcheck/tests/runTests.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.

> require("gDNAx") || stop("unable to load gDNAx package")
Loading required package: gDNAx
[1] TRUE
> BiocGenerics:::testPackage("gDNAx")

Attaching package: 'BiocGenerics'

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, aperm, 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: GenomicFeatures
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
require("Rsamtools")
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

The following object is masked from 'package:Biobase':

    rowMedians

Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

The following object is masked from 'package:Biobase':

    cache

see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
Fetching annotations for hg38
Start processing BAM file(s)
Computing strandedness from s32gDNA0.bam
Computing strandedness from s33gDNA0.bam


RUNIT TEST PROTOCOL -- Tue Apr 16 03:24:00 2024 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gDNAx RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
194.538  15.465 262.020 

Example timings

gDNAx.Rcheck/gDNAx-Ex.timings

nameusersystemelapsed
filterBAMtx141.497 11.642195.774
gDNAdx125.468 6.441147.100
gDNAx-class0.1130.0070.138
strandedness58.529 3.17474.041