Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1898/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scrapper 1.0.3  (landing page)
Aaron Lun
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/scrapper
git_branch: RELEASE_3_20
git_last_commit: 732a984
git_last_commit_date: 2024-12-17 21:32:23 -0500 (Tue, 17 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  YES


CHECK results for scrapper on merida1

To the developers/maintainers of the scrapper package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scrapper.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.

raw results


Summary

Package: scrapper
Version: 1.0.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scrapper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scrapper_1.0.3.tar.gz
StartedAt: 2024-12-20 09:21:50 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 09:27:54 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 364.4 seconds
RetCode: 0
Status:   OK  
CheckDir: scrapper.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scrapper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scrapper_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scrapper.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.0.3’
* 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 ‘scrapper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 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
runAllNeighborSteps 0.166  0.013  12.843
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/scrapper.Rcheck/00check.log’
for details.


Installation output

scrapper.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scrapper
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘scrapper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c adt_quality_control.cpp -o adt_quality_control.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c aggregate_across_cells.cpp -o aggregate_across_cells.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c build_snn_graph.cpp -o build_snn_graph.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c center_size_factors.cpp -o center_size_factors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c choose_pseudo_count.cpp -o choose_pseudo_count.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cluster_graph.cpp -o cluster_graph.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cluster_kmeans.cpp -o cluster_kmeans.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c combine_factors.cpp -o combine_factors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c correct_mnn.cpp -o correct_mnn.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c crispr_quality_control.cpp -o crispr_quality_control.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fit_variance_trend.cpp -o fit_variance_trend.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c model_gene_variances.cpp -o model_gene_variances.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c normalize_counts.cpp -o normalize_counts.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rna_quality_control.cpp -o rna_quality_control.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c run_pca.cpp -o run_pca.o
In file included from run_pca.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/scran_pca/scran_pca.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/scran_pca/simple_pca.hpp:7:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/irlba/parallel.hpp:444:9: warning: private field 'my_previous' is not used [-Wunused-private-field]
    int my_previous;
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c run_tsne.cpp -o run_tsne.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c run_umap.cpp -o run_umap.o
In file included from run_umap.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/umappp/umappp.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/umappp/initialize.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/umappp/spectral_init.hpp:5:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/irlba/parallel.hpp:444:9: warning: private field 'my_previous' is not used [-Wunused-private-field]
    int my_previous;
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sanitize_size_factors.cpp -o sanitize_size_factors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c scale_by_neighbors.cpp -o scale_by_neighbors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c score_gene_set.cpp -o score_gene_set.o
In file included from score_gene_set.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/gsdecon/gsdecon.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/gsdecon/compute.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/scran_pca/scran_pca.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/scran_pca/simple_pca.hpp:7:
/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include/irlba/parallel.hpp:444:9: warning: private field 'my_previous' is not used [-Wunused-private-field]
    int my_previous;
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c score_markers.cpp -o score_markers.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c summarize_effects.cpp -o summarize_effects.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.o build_snn_graph.o center_size_factors.o choose_highly_variable_genes.o choose_pseudo_count.o cluster_graph.o cluster_kmeans.o combine_factors.o compute_clrm1_factors.o correct_mnn.o crispr_quality_control.o fit_variance_trend.o model_gene_variances.o normalize_counts.o rna_quality_control.o run_pca.o run_tsne.o run_umap.o sanitize_size_factors.o scale_by_neighbors.o score_gene_set.o score_markers.o subsample_by_neighbors.o summarize_effects.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-scrapper/00new/scrapper/libs
** R
** 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 (scrapper)

Tests output

scrapper.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 647 ]
> 
> proc.time()
   user  system elapsed 
 27.038   1.483 102.327 

Example timings

scrapper.Rcheck/scrapper-Ex.timings

nameusersystemelapsed
adt_quality_control0.1010.0060.111
aggregateAcrossCells0.0620.0070.074
buildSnnGraph0.7170.0250.783
centerSizeFactors0.0020.0030.005
chooseHighlyVariableGenes0.0010.0010.002
choosePseudoCount0.0010.0010.002
clusterGraph1.4350.0291.540
clusterKmeans0.0030.0010.004
combineFactors0.0090.0040.013
computeClrm1Factors0.0270.0020.031
correctMnn0.9840.0071.046
crispr_quality_control0.0260.0020.031
fitVarianceTrend0.0200.0040.025
modelGeneVariances0.0840.0060.092
normalizeCounts0.2620.0040.275
rna_quality_control0.0350.0040.039
runAllNeighborSteps 0.166 0.01312.843
runPca0.2020.0050.211
runTsne0.3460.0040.355
runUmap0.3120.0030.317
sanitizeSizeFactors0.0020.0030.004
scaleByNeighbors0.1460.0010.148
scoreGeneSet0.1090.0040.114
scoreMarkers0.1520.0070.160
subsampleByNeighbors2.1640.0222.244
summarizeEffects0.1500.0160.166