Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1973/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
single 1.10.0  (landing page)
Rocio Espada
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/single
git_branch: RELEASE_3_20
git_last_commit: 00b3c6f
git_last_commit_date: 2024-10-29 11:09:56 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for single on kunpeng2

To the developers/maintainers of the single package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: single
Version: 1.10.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:single.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings single_1.10.0.tar.gz
StartedAt: 2024-11-20 12:32:05 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 12:36:17 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 252.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: single.Rcheck
Warnings: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:single.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings single_1.10.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/single.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘single/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘single’ version ‘1.10.0’
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 .load_package_gracefully("pwalign", "starting with BioC 3.19, ",  : 
  Could not load package pwalign. Is it installed?

  Note that starting with BioC 3.19, calling compareStrings() requires
  the pwalign package. Please install it with:

    BiocManager::install("pwalign")
Calls: list_mismatches ... <Anonymous> -> .call_fun_in_pwalign -> .load_package_gracefully
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/single.Rcheck/00check.log’
for details.


Installation output

single.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL single
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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
Warning in fun(libname, pkgname) :
  Package 'single' is deprecated and will be removed from Bioconductor
  version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'single' is deprecated and will be removed from Bioconductor
  version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (single)

Tests output


Example timings

single.Rcheck/single-Ex.timings

nameusersystemelapsed
evaluate_fits0.1260.0120.139
fit_logregr5.0900.2795.385
glm.predict.0.0030.0000.003