Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:05:38 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 conclus on nebbiolo1


To the developers/maintainers of the conclus package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/conclus.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 382/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
conclus 1.3.1  (landing page)
Ilyess Rachedi
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/conclus
git_branch: master
git_last_commit: 97afbff
git_last_commit_date: 2021-12-02 09:57:38 -0500 (Thu, 02 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: conclus
Version: 1.3.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:conclus.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings conclus_1.3.1.tar.gz
StartedAt: 2022-01-21 18:44:08 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 18:48:51 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 283.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: conclus.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:conclus.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings conclus_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/conclus.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘conclus/DESCRIPTION’ ... OK
* this is package ‘conclus’ version ‘1.3.1’
* 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 ‘conclus’ 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 ... WARNING
'::' or ':::' import not declared from: ‘DT’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.removeNoSymbol: no visible binding for global variable ‘SYMBOL’
Undefined global functions or variables:
  SYMBOL
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'clusterCellsInternal,scRNAseq-method':
clusterCellsInternal
  Code: function(theObject, clusterNumber = NULL, deepSplit = 4, cores
                 = 2, clusteringMethod = "ward.D2")
  Docs: function(theObject, clusterNumber = 0, deepSplit = 4, cores =
                 2, clusteringMethod = "ward.D2")
  Mismatches in argument default values:
    Name: 'clusterNumber' Code: NULL Docs: 0

Codoc mismatches from documentation object 'normaliseCountMatrix,scRNAseq-method':
normaliseCountMatrix
  Code: function(theObject, sizes = c(20, 40, 60, 80, 100), rowdata =
                 NULL, coldata = NULL, alreadyCellFiltered = FALSE,
                 runQuickCluster = TRUE, info = TRUE, removeNoSymbol =
                 FALSE)
  Docs: function(theObject, sizes = c(20, 40, 60, 80, 100), rowdata =
                 NULL, coldata = NULL, alreadyCellFiltered = FALSE,
                 runQuickCluster = TRUE, info = TRUE)
  Argument names in code not in docs:
    removeNoSymbol

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'getters'
  ‘cluster’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘conclus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addClustering,scRNAseq-method
> ### Title: addClustering
> ### Aliases: addClustering,scRNAseq-method addClustering
> 
> ### ** Examples
> 
> ## Object scr containing the results of previous steps
> load(system.file("extdata/scrFull.Rdat", package="conclus"))
> 
> ## Retrieving the table indicating to which cluster each cell belongs
> clustCellsDf <- retrieveTableClustersCells(scr)
Error in validObject(theObject) : 
  invalid class “scRNAseq” object: slots in class definition but not in object: "topMarkers"
Calls: retrieveTableClustersCells -> retrieveTableClustersCells -> validObject
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─conclus::`setGenesInfos<-`(...)
    7. └─conclus::`setGenesInfos<-`(...)
    8.   └─methods::validObject(theObject)
    9.     ├─methods:::anyStrings(validityMethod(object))
   10.     │ └─base::isTRUE(x)
   11.     └─conclus:::validityMethod(object)
   12.       └─conclus:::.testGenesInfosSlot(object)
   13.         └─conclus:::checkGenesInfos(genesInfos, species, clustersSimiliratyOrdered)
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 76 ]
  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: 2 ERRORs, 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/conclus.Rcheck/00check.log’
for details.


Installation output

conclus.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘conclus’ ...
** 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 (conclus)

Tests output

conclus.Rcheck/tests/test-all.Rout.fail


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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("conclus")


Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

> test_check("conclus")
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 76 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_getters.R:89:5): getClustersMarkers works properly ──────────────
Error in `getClustersMarkers(scr)`: could not find function "getClustersMarkers"
Backtrace:
    █
 1. └─testthat::expect_equal(getClustersMarkers(scr), df) test_getters.R:89:4
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))
── Error (test_scRNAseq-methods.R:55:1): (code run outside of `test_that()`) ───
Error in `ans[ypos] <- rep(yes, length.out = len)[ypos]`: replacement has length zero
Backtrace:
    █
 1. ├─conclus::normaliseCountMatrix(...) test_scRNAseq-methods.R:55:0
 2. └─conclus::normaliseCountMatrix(...)
 3.   └─base::ifelse(...)
── Error (test_setters.R:251:5): clustersMarkers works properly ────────────────
Error in `setClustersMarkers(scr) <- newDF`: could not find function "setClustersMarkers<-"
── Failure (test_setters.R:314:5): genesInfos works properly ───────────────────
`setGenesInfos(scr) <- wrongDF` threw an error with unexpected message.
Expected match: "The genesInfos data frame should have the columns: uniprot_gn_symbol;clusters;external_gene_name;go_id;entrezgene_description;gene_biotype;chromosome_name;Symbol;ensembl_gene_id;entrezgene_id;uniprot_gn_id;mgi_description;mgi_id"
Actual message: "The genesInfos data frame should have the columns: uniprot_gn_symbol;clusters;go_id;entrezgene_description;gene_biotype;chromosome_name;Symbol;ensembl_gene_id;entrezgene_id;uniprot_gn_id;mgi_description;mgi_id"
Backtrace:
     █
  1. ├─testthat::expect_error(setGenesInfos(scr) <- wrongDF, regexp = expM) test_setters.R:314:4
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat:::.capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─conclus::`setGenesInfos<-`(...)
  7. └─conclus::`setGenesInfos<-`(...)
  8.   └─methods::validObject(theObject)
  9.     ├─methods:::anyStrings(validityMethod(object))
 10.     │ └─base::isTRUE(x)
 11.     └─conclus:::validityMethod(object)
 12.       └─conclus:::.testGenesInfosSlot(object)
 13.         └─conclus:::checkGenesInfos(genesInfos, species, clustersSimiliratyOrdered)

[ FAIL 4 | WARN 1 | SKIP 0 | PASS 76 ]
Error: Test failures
Execution halted

Example timings

conclus.Rcheck/conclus-Ex.timings

nameusersystemelapsed