Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-12-06 11:06:50 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4506
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4283
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4312
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 Rcade on nebbiolo2


To the developers/maintainers of the Rcade package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rcade.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 1608/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcade 1.40.0  (landing page)
Jonathan Cairns
Snapshot Date: 2022-12-05 14:00:06 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/Rcade
git_branch: RELEASE_3_16
git_last_commit: 2290b0f
git_last_commit_date: 2022-11-01 11:07:31 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    ERROR    OK  

Summary

Package: Rcade
Version: 1.40.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Rcade.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings Rcade_1.40.0.tar.gz
StartedAt: 2022-12-05 23:00:41 -0500 (Mon, 05 Dec 2022)
EndedAt: 2022-12-05 23:05:42 -0500 (Mon, 05 Dec 2022)
EllapsedTime: 301.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Rcade.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Rcade.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings Rcade_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Rcade.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘Rcade/DESCRIPTION’ ... OK
* this is package ‘Rcade’ version ‘1.40.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rcade’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'Rcade' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.16-bioc/meat/Rcade.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* 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 ... NOTE
constructRcadeTable: no visible binding for global variable ‘p.DE’
constructRcadeTable: no visible binding for global variable ‘p.ChIP’
plotBBB,Rcade: no visible global function definition for ‘decorate3d’
Undefined global functions or variables:
  decorate3d p.ChIP p.DE
* 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
RcadeAnalysis    5.969  0.292   6.271
diffCountsBaySeq 5.512  0.092   5.604
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  
   
  1 Test Suite : 
  Rcade RUnit Tests - 3 test functions, 1 error, 0 failures
  ERROR in test_constructRcadeTable: Error in target == current : comparison of these types is not implemented
  
  Test files with failing tests
  
     test_modules.R 
       test_constructRcadeTable 
  
  
  Error in BiocGenerics:::testPackage("Rcade") : 
    unit tests failed for package Rcade
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Rcade.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/Rcade.Rcheck/00check.log’
for details.


Installation output

Rcade.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL Rcade
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘Rcade’ ...
** 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
Warning: Package 'Rcade' is deprecated and will be removed from Bioconductor
  version 3.17
** testing if installed package can be loaded from final location
Warning: Package 'Rcade' is deprecated and will be removed from Bioconductor
  version 3.17
** testing if installed package keeps a record of temporary installation path
* DONE (Rcade)

Tests output

Rcade.Rcheck/tests/runTests.Rout.fail


R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
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.

> require("Rcade") || stop("unable to load Rcade")
Loading required package: Rcade
Loading required package: GenomicRanges
Loading required package: stats4
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: baySeq
Loading required package: abind
Loading required package: parallel
Welcome to Rcade - version 1.40.0
If you are new to Rcade, please consider reading the vignette through the command: vignette("Rcade").

Attaching package: 'Rcade'

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

    plotPCA

[1] TRUE
Warning message:
Package 'Rcade' is deprecated and will be removed from Bioconductor
  version 3.17 
> BiocGenerics:::testPackage("Rcade")
Timing stopped at: 0.026 0 0.025
Error in target == current : comparison of these types is not implemented
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Found 24 chromosomes, of which 0 are present in the annotation.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Removed all instances of 'chr' - now 19 chromosomes are present in the annotation.
File wgEncodeSydhTfbsHelas3InputIfng30StdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3InputStdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep1.bam: Counting reads.
File wgEncodeSydhTfbsHelas3Stat1Ifng30StdAlnRep2.bam: Counting reads.


RUNIT TEST PROTOCOL -- Mon Dec  5 23:05:01 2022 
*********************************************** 
Number of test functions: 3 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
Rcade RUnit Tests - 3 test functions, 1 error, 0 failures
ERROR in test_constructRcadeTable: Error in target == current : comparison of these types is not implemented

Test files with failing tests

   test_modules.R 
     test_constructRcadeTable 


Error in BiocGenerics:::testPackage("Rcade") : 
  unit tests failed for package Rcade
Execution halted

Example timings

Rcade.Rcheck/Rcade-Ex.timings

nameusersystemelapsed
Rcade-class0.3300.0330.359
RcadeAnalysis5.9690.2926.271
RcadeSTAT10.0040.0000.004
constructRcadeTable0.0080.0000.008
countReads3.6610.1283.790
defineBins0.0170.0000.016
diffCountsBaySeq5.5120.0925.604
exportRcade-methods0.0010.0000.002