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This page was generated on 2024-02-02 12:51:39 -0500 (Fri, 02 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4620
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4362
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4389
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4324
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 1737/2237HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RLSeq 1.9.0  (landing page)
Henry Miller
Snapshot Date: 2024-02-01 14:00:18 -0500 (Thu, 01 Feb 2024)
git_url: https://git.bioconductor.org/packages/RLSeq
git_branch: devel
git_last_commit: d66b911
git_last_commit_date: 2023-10-24 11:38:24 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for RLSeq on nebbiolo1


To the developers/maintainers of the RLSeq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RLSeq.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: RLSeq
Version: 1.9.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RLSeq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RLSeq_1.9.0.tar.gz
StartedAt: 2024-02-02 00:57:46 -0500 (Fri, 02 Feb 2024)
EndedAt: 2024-02-02 01:15:23 -0500 (Fri, 02 Feb 2024)
EllapsedTime: 1057.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RLSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RLSeq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RLSeq_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RLSeq.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RLSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RLSeq’ version ‘1.9.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RLSeq’ 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
report               55.716  3.780  60.623
RLSeq                32.573  1.272  36.164
predictCondition     15.409  0.400  16.357
plotEnrichment       13.672  0.296  14.180
txFeatureOverlap     10.736  0.492  11.354
plotRLRegionOverlap   9.350  0.655  10.805
geneAnnotation        8.764  0.496   9.840
featureEnrich         8.744  0.221   9.147
corrHeatmap           6.926  0.652   7.667
plotTxFeatureOverlap  5.983  0.504   6.880
RLRangesFromRLBase    3.986  0.233   5.422
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

RLSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RLSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘RLSeq’ ...
** using staged installation
** R
** data
** 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 (RLSeq)

Tests output

RLSeq.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(RLSeq)
> 
> test_check("RLSeq")
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
[1] "Note: The minimum p-value with only 30 permutations is 0.032258064516129. You should consider increasing the number of permutations."
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
Loading required package: GenomicFeatures
Loading required package: BiocGenerics

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, table, tapply,
    union, unique, unsplit, which.max, which.min

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")'.

  2135 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
see ?RLHub and browseVignettes('RLHub') for documentation
[1] "Note: The minimum p-value with only 30 permutations is 0.032258064516129. You should consider increasing the number of permutations."
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
see ?RLHub and browseVignettes('RLHub') for documentation
  2135 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
see ?RLHub and browseVignettes('RLHub') for documentation
[ FAIL 0 | WARN 136 | SKIP 0 | PASS 8 ]

[ FAIL 0 | WARN 136 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
277.457  25.687 320.324 

Example timings

RLSeq.Rcheck/RLSeq-Ex.timings

nameusersystemelapsed
RLRanges0.8130.0272.188
RLRangesFromRLBase3.9860.2335.422
RLResults0.1850.0080.195
RLSeq32.573 1.27236.164
analyzeRLFS2.3770.0593.265
auxdata0.1130.0000.113
available_genomes0.0200.0360.056
corrAnalyze3.4180.0694.386
corrHeatmap6.9260.6527.667
featureEnrich8.7440.2219.147
geneAnnotation8.7640.4969.840
genomeMasks0.0820.0000.083
noiseAnalyze0.6120.0161.330
noiseComparisonPlot4.2640.1164.653
plotEnrichment13.672 0.29614.180
plotFingerprint0.2620.0080.270
plotRLFSRes0.4840.0040.488
plotRLRegionOverlap 9.350 0.65510.805
plotTxFeatureOverlap5.9830.5046.880
predictCondition15.409 0.40016.357
randomWindows0.0530.0040.058
report55.716 3.78060.623
rlRegionTest4.0790.2644.518
rlbaseNoiseAnalyze0.0100.0040.015
rlsampleTxOl0.020.000.02
txFeatureOverlap10.736 0.49211.354