Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:19 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 single on nebbiolo2


To the developers/maintainers of the single package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/single.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 1886/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
single 1.2.0  (landing page)
Rocio Espada
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/single
git_branch: RELEASE_3_16
git_last_commit: c6b958b
git_last_commit_date: 2023-01-18 05:18:57 -0400 (Wed, 18 Jan 2023)
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: single
Version: 1.2.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:single.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings single_1.2.0.tar.gz
StartedAt: 2023-04-11 00:04:09 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:07:43 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 214.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: single.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:single.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings single_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/single.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘single/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘single’ 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 ‘single’ 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 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
pileup_by_QUAL: no visible binding for global variable ‘count.y’
pileup_by_QUAL: no visible binding for global variable ‘count.x’
pileup_by_QUAL: no visible binding for global variable ‘nucleotide’
pileup_by_QUAL: no visible binding for global variable ‘QUAL’
single_consensus_byBarcode: no visible binding for global variable
  ‘readID’
single_consensus_byBarcode: no visible binding for global variable
  ‘bcID’
Undefined global functions or variables:
  QUAL bcID count.x count.y nucleotide readID
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘single-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: list_mismatches
> ### Title: Lists mismatches between two DNAstrings
> ### Aliases: list_mismatches
> 
> ### ** Examples
> 
> ref = Biostrings::DNAString("AAAA")
> seq = Biostrings::DNAString("AGAT")
> list_mismatches(ref,seq)
Error in `stringr::str_sub()`:
! `string` must be a vector, not a <DNAString> object.
Backtrace:
    ▆
 1. ├─single::list_mismatches(ref, seq)
 2. │ └─base::sapply(...)
 3. │   └─base::lapply(X = X, FUN = FUN, ...)
 4. │     └─single (local) FUN(X[[i]], ...)
 5. │       └─stringr::str_sub(ref, x)
 6. │         └─vctrs::vec_size_common(string = string, start = start, end = end)
 7. └─vctrs:::stop_scalar_type(`<fn>`(`<DNAStrng>`), "string", `<env>`)
 8.   └─vctrs:::stop_vctrs(...)
 9.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘single.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/single.Rcheck/00check.log’
for details.


Installation output

single.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘single’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (single)

Tests output


Example timings

single.Rcheck/single-Ex.timings

nameusersystemelapsed
evaluate_fits0.1160.0320.148
fit_logregr5.1430.2965.439
glm.predict.0.0000.0030.003