Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:47 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for RLSeq on nebbiolo1


To the developers/maintainers of the RLSeq package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1664/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RLSeq 1.2.0  (landing page)
Henry Miller
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/RLSeq
git_branch: RELEASE_3_15
git_last_commit: 7afa0ea
git_last_commit_date: 2022-04-26 12:20:01 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: RLSeq
Version: 1.2.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RLSeq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RLSeq_1.2.0.tar.gz
StartedAt: 2022-10-18 21:30:39 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:40:41 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 601.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: RLSeq.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RLSeq.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RLSeq_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RLSeq.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RLSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RLSeq’ version ‘1.2.0’
* 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 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              47.563  3.991  53.173
RLSeq               19.975  1.512  22.757
predictCondition    16.420  1.940  18.929
featureEnrich       12.709  1.092  14.012
plotEnrichment      10.716  1.069  12.081
geneAnnotation       9.246  1.205  11.079
plotRLRegionOverlap  8.694  1.257  10.859
corrHeatmap          6.243  0.584   6.925
RLRangesFromRLBase   4.511  0.839   6.557
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  see ?RLHub and browseVignettes('RLHub') for documentation
  [ FAIL 1 | WARN 116 | SKIP 0 | PASS 6 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plotEnrichment.R:15'): Test plotEnrichment ───────────────────
  warns\[1\] does not match "User-supplied sample test value is NA for .*".
  Actual value: "Use of \.data in tidyselect expressions was deprecated in tidyselect 1\.2\.0\.\\ni Please use `"db"` instead of `\.data\$db`"
  Backtrace:
      ▆
   1. └─testthat::expect_match(warns[1], regexp = "User-supplied sample test value is NA for .*") at test-plotEnrichment.R:15:4
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 1 | WARN 116 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
* 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 ERROR
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/RLSeq.Rcheck/00check.log’
for details.


Installation output

RLSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RLSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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.fail


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(RLSeq)
> 
> test_check("RLSeq")
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, 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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

snapshotDate(): 2022-04-26
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 10 permutations is 0.0909090909090909. 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
snapshotDate(): 2022-04-25
Loading required package: GenomicFeatures
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")'.

  1662 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 10 permutations is 0.0909090909090909. 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
snapshotDate(): 2022-04-25
  1662 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 1 | WARN 116 | SKIP 0 | PASS 6 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotEnrichment.R:15'): Test plotEnrichment ───────────────────
warns\[1\] does not match "User-supplied sample test value is NA for .*".
Actual value: "Use of \.data in tidyselect expressions was deprecated in tidyselect 1\.2\.0\.\\ni Please use `"db"` instead of `\.data\$db`"
Backtrace:
    ▆
 1. └─testthat::expect_match(warns[1], regexp = "User-supplied sample test value is NA for .*") at test-plotEnrichment.R:15:4
 2.   └─testthat:::expect_match_(...)

[ FAIL 1 | WARN 116 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted

Example timings

RLSeq.Rcheck/RLSeq-Ex.timings

nameusersystemelapsed
RLRanges0.5910.0231.956
RLRangesFromRLBase4.5110.8396.557
RLResults0.1420.0160.161
RLSeq19.975 1.51222.757
analyzeRLFS2.4930.2853.856
auxdata0.0730.0190.092
available_genomes0.0250.0400.065
corrAnalyze3.5070.2914.863
corrHeatmap6.2430.5846.925
featureEnrich12.709 1.09214.012
geneAnnotation 9.246 1.20511.079
genomeMasks0.0730.0080.081
plotEnrichment10.716 1.06912.081
plotRLFSRes0.4050.0240.428
plotRLRegionOverlap 8.694 1.25710.859
predictCondition16.420 1.94018.929
report47.563 3.99153.173
rlRegionTest3.9450.4794.632