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This page was generated on 2023-11-02 11:40:24 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 53/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alevinQC 1.18.0  (landing page)
Charlotte Soneson
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/alevinQC
git_branch: RELEASE_3_18
git_last_commit: 5ae6143
git_last_commit_date: 2023-10-24 11:11:09 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for alevinQC on kunpeng2


To the developers/maintainers of the alevinQC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alevinQC.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: alevinQC
Version: 1.18.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:alevinQC.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings alevinQC_1.18.0.tar.gz
StartedAt: 2023-11-02 08:16:18 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 08:19:49 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 211.1 seconds
RetCode: 0
Status:   OK  
CheckDir: alevinQC.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:alevinQC.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings alevinQC_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/alevinQC.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘alevinQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alevinQC’ version ‘1.18.0’
* 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 ‘alevinQC’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 20.5Mb
  sub-directories of 1Mb or more:
    extdata  19.3Mb
* 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 ... 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 C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
qcReport 23.032   0.54  24.367
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/alevinQC.Rcheck/00check.log’
for details.



Installation output

alevinQC.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL alevinQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘alevinQC’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c convert_permit_freq.cpp -o convert_permit_freq.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o alevinQC.so RcppExports.o convert_permit_freq.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-alevinQC/00new/alevinQC/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (alevinQC)

Tests output

alevinQC.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(alevinQC)
> 
> test_check("alevinQC")
100% of barcodes in custom barcode set set2 were found in the data set (100% were quantified)
100% of barcodes in custom barcode set set2 were found in the data set (100% were quantified)
The magick package is required to crop "tmp2_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "tmp2_files/figure-html/unnamed-chunk-11-1.png" but not available.
The magick package is required to crop "tmp2_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "tmp2_files/figure-html/unnamed-chunk-17-1.png" but not available.
The magick package is required to crop "tmp2_files/figure-html/unnamed-chunk-18-1.png" but not available.
100% of barcodes in custom barcode set set1 were found in the data set (100% were quantified)
100% of barcodes in custom barcode set set2 were found in the data set (100% were quantified)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 274 ]
> 
> proc.time()
   user  system elapsed 
118.680   4.221 127.961 

Example timings

alevinQC.Rcheck/alevinQC-Ex.timings

nameusersystemelapsed
checkAlevinFryInputFiles0.0050.0000.007
checkAlevinInputFiles0.0020.0000.004
plotAlevinBarcodeCollapse1.5990.0881.709
plotAlevinHistogram1.0530.0041.059
plotAlevinKneeNbrGenes0.9920.0040.998
plotAlevinKneeRaw2.7550.0802.842
plotAlevinQuant1.7100.0041.719
plotAlevinQuantPairs2.9040.0442.955
qcReport23.032 0.54024.367
qcShiny1.7750.0481.839
readAlevinFryQC0.4140.0040.419
readAlevinQC0.6350.0280.665