Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-15 13:20:44 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 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 20.04.4 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

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: 2022-08-14 21:39:10 -0400 (Sun, 14 Aug 2022)
EndedAt: 2022-08-14 21:48:38 -0400 (Sun, 14 Aug 2022)
EllapsedTime: 567.7 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              45.473  3.952  51.042
RLSeq               19.799  1.359  22.567
predictCondition    14.513  1.218  16.210
featureEnrich       12.434  0.673  13.370
plotEnrichment      10.409  0.821  11.565
geneAnnotation       9.071  1.167  10.895
plotRLRegionOverlap  8.739  1.185  10.614
corrHeatmap          7.100  0.748   7.950
rlRegionTest         5.343  1.148   6.765
RLRangesFromRLBase   3.450  0.512   5.108
corrAnalyze          3.198  0.295   5.061
* 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:
  ── Error (test-rlseq.R:7:5): Test that RLSeq works ─────────────────────────────
  Error in `predictCondition(object)`: Found Inf values in Z score distribution. Set 'ntimes' higher in analyzeRLFS
  Backtrace:
      ▆
   1. ├─testthat::expect_s4_class(...) at test-rlseq.R:7:4
   2. │ ├─testthat:::format_class(methods::is(object))
   3. │ │ ├─base::paste0(encodeString(x, quote = "'"), collapse = "/")
   4. │ │ └─base::encodeString(x, quote = "'")
   5. │ └─methods::is(object)
   6. └─RLSeq::RLSeq(object = rlr, quiet = TRUE, useMask = FALSE, ntimes = 10)
   7.   └─RLSeq::predictCondition(object)
  
  [ FAIL 1 | WARN 37 | 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
[ FAIL 1 | WARN 37 | SKIP 0 | PASS 6 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test-rlseq.R:7:5): Test that RLSeq works ─────────────────────────────
Error in `predictCondition(object)`: Found Inf values in Z score distribution. Set 'ntimes' higher in analyzeRLFS
Backtrace:
    ▆
 1. ├─testthat::expect_s4_class(...) at test-rlseq.R:7:4
 2. │ ├─testthat:::format_class(methods::is(object))
 3. │ │ ├─base::paste0(encodeString(x, quote = "'"), collapse = "/")
 4. │ │ └─base::encodeString(x, quote = "'")
 5. │ └─methods::is(object)
 6. └─RLSeq::RLSeq(object = rlr, quiet = TRUE, useMask = FALSE, ntimes = 10)
 7.   └─RLSeq::predictCondition(object)

[ FAIL 1 | WARN 37 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted

Example timings

RLSeq.Rcheck/RLSeq-Ex.timings

nameusersystemelapsed
RLRanges0.5080.0801.724
RLRangesFromRLBase3.4500.5125.108
RLResults0.1390.0280.169
RLSeq19.799 1.35922.567
analyzeRLFS2.4220.3123.723
auxdata0.0860.0000.087
available_genomes0.0210.0440.064
corrAnalyze3.1980.2955.061
corrHeatmap7.1000.7487.950
featureEnrich12.434 0.67313.370
geneAnnotation 9.071 1.16710.895
genomeMasks0.0780.0120.090
plotEnrichment10.409 0.82111.565
plotRLFSRes0.4050.0140.419
plotRLRegionOverlap 8.739 1.18510.614
predictCondition14.513 1.21816.210
report45.473 3.95251.042
rlRegionTest5.3431.1486.765