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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 1881/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scifer 1.8.0  (landing page)
Rodrigo Arcoverde Cerveira
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/scifer
git_branch: RELEASE_3_20
git_last_commit: 50dc6b9
git_last_commit_date: 2024-10-29 11:14:21 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
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    OK  


CHECK results for scifer on kunpeng2

To the developers/maintainers of the scifer package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scifer.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: scifer
Version: 1.8.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scifer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scifer_1.8.0.tar.gz
StartedAt: 2024-11-20 12:10:42 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 12:20:36 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 594.0 seconds
RetCode: 0
Status:   OK  
CheckDir: scifer.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scifer.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scifer_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scifer.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 ‘scifer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scifer’ version ‘1.8.0’
* 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 ‘scifer’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/biocbuild/bbs-3.20-bioc/meat/scifer.Rcheck/00install.out’ for details.
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New igblast wrapper function to run igblast on fasta sequences
    igblast function returns the output from a local igblast run with any custom database
    New function requires additional steps for ARM processors, please read the README
* 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘secondary_peaks’
* 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
quality_report     84.283  0.642  85.196
summarise_quality  74.336  0.603  75.409
summarise_abi_file 23.482  0.195  23.725
secondary_peaks    22.952  0.483  23.594
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scifer.Rcheck/00check.log’
for details.


Installation output

scifer.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘scifer’ ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scifer)

Tests output

scifer.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(scifer)
> 
> test_check("scifer")


processing file: HC_report.Rmd
output file: HC_report.knit.md

/home/biocbuild/bin/pandoc +RTS -K512m -RTS HC_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/tmp/RtmpvG7USw/QC_report.html --lua-filter /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/biocbuild/R/R-4.4.1/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /home/biocbuild/tmp/RtmpvG7USw/rmarkdown-str202e6610718f8c.html 

Output created: /home/biocbuild/tmp/RtmpvG7USw/QC_report.html
[ FAIL 0 | WARN 7 | SKIP 4 | PASS 49 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• This test is not supported on Linux with arm architecture. (4):
  'test-igblast.R:18:5', 'test-igblast.R:40:5', 'test-igblast.R:66:5',
  'test-igblast.R:76:3'

[ FAIL 0 | WARN 7 | SKIP 4 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
215.562   1.106 217.079 

Example timings

scifer.Rcheck/scifer-Ex.timings

nameusersystemelapsed
df_to_fasta0.0450.0000.046
fcs_plot0.3680.0200.393
fcs_processing0.1880.0160.204
igblast000
quality_report84.283 0.64285.196
secondary_peaks22.952 0.48323.594
summarise_abi_file23.482 0.19523.725
summarise_quality74.336 0.60375.409