Multiple platform build/check report for BioC 3.23 - CHECK results for scrapper on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4917
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences"	4629
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 scrapper on kjohnson3

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: 1.5.16

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_1.5.16.tar.gz

StartedAt: 2026-04-09 20:03:14 -0400 (Thu, 09 Apr 2026)

EndedAt: 2026-04-09 20:05:37 -0400 (Thu, 09 Apr 2026)

EllapsedTime: 142.6 seconds

RetCode: 1

Status: ERROR

CheckDir: scrapper.Rcheck

Warnings: NA

Command output

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### 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_1.5.16.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/scrapper.Rcheck’
* using R Under development (unstable) (2026-03-26 r89717)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-10 00:03:14 UTC
* using option ‘--no-vignettes’
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.5.16’
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘assorthead’ is only usable in R >= 3.0.2
Package in 'LinkingTo' providing no 'include' directory:
  ‘Rigraphlib’
* 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 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 ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/scrapper/libs/scrapper.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘scrapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildSnnGraph
> ### Title: Build a shared nearest neighbor graph
> ### Aliases: buildSnnGraph
> 
> ### ** Examples
> 
> data <- matrix(rnorm(10000), ncol=1000)
> out <- buildSnnGraph(data)
> str(out)
List of 3
 $ vertices: int 1000
 $ edges   : int [1:106118] 3 2 4 2 7 4 7 2 7 5 ...
 $ weights : num [1:53059] 4.5 5.5 5 6 4.5 4 1.5 3 4.5 3 ...
> 
> # We can use this to make an igraph::graph.
> g <- igraph::make_undirected_graph(out$edges, n = out$vertices)
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
Calls: loadNamespace -> library.dynam -> dyn.load
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
aggregateAcrossCells.se 6.471  0.158   6.676
analyze.se              3.484  0.071   7.143
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. └─base::loadNamespace(x) at test-clusterGraph.R:34:5
   2.   └─base::library.dynam(lib, package, package.lib)
   3.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
  ── Error ('test-normalizeCounts.R:12:5'): normalizeCounts gives the same results in all modes ──
  Error in `eval_bare(expr, quo_get_env(quo))`: object 'tatami_row' not found
  Backtrace:
      ▆
   1. └─testthat::expect_equal(y[1, ], beachmat:::tatami_row(z, 1)) at test-normalizeCounts.R:12:5
   2.   └─testthat::quasi_label(enquo(expected), expected.label)
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1317 ]
  Error:
  ! Test failures.
  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: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/scrapper.Rcheck/00check.log’
for details.

Installation output

scrapper.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘scrapper’ ...
** this is package ‘scrapper’ version ‘1.5.16’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++17
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c adt_quality_control.cpp -o adt_quality_control.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c aggregate_across_cells.cpp -o aggregate_across_cells.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c aggregate_across_genes.cpp -o aggregate_across_genes.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c build_snn_graph.cpp -o build_snn_graph.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c center_size_factors.cpp -o center_size_factors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c choose_pseudo_count.cpp -o choose_pseudo_count.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cluster_graph.cpp -o cluster_graph.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cluster_kmeans.cpp -o cluster_kmeans.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c combine_factors.cpp -o combine_factors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c compute_block_weights.cpp -o compute_block_weights.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c correct_mnn.cpp -o correct_mnn.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c crispr_quality_control.cpp -o crispr_quality_control.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fit_variance_trend.cpp -o fit_variance_trend.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c model_gene_variances.cpp -o model_gene_variances.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c normalize_counts.cpp -o normalize_counts.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rna_quality_control.cpp -o rna_quality_control.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c run_pca.cpp -o run_pca.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c run_tsne.cpp -o run_tsne.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c run_umap.cpp -o run_umap.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sanitize_size_factors.cpp -o sanitize_size_factors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c scale_by_neighbors.cpp -o scale_by_neighbors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c score_gene_set.cpp -o score_gene_set.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c score_markers.cpp -o score_markers.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c set_executor.cpp -o set_executor.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c summarize_effects.cpp -o summarize_effects.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test_enrichment.cpp -o test_enrichment.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.o aggregate_across_genes.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_block_weights.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 set_executor.o subsample_by_neighbors.o summarize_effects.o test_enrichment.o /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rigraphlib/igraph/lib/libigraph.a -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-scrapper/00new/scrapper/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 (scrapper)

Tests output

scrapper.Rcheck/tests/testthat.Rout.fail


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Platform: aarch64-apple-darwin23

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> library(testthat)
> library(scrapper)
> test_check("scrapper")
Saving _problems/test-clusterGraph-34.R
Saving _problems/test-normalizeCounts-12.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1317 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-clusterGraph.R:34:5'): clusterGraph works correctly for multilevel ──
Error in `dyn.load(file, DLLpath = DLLpath, ...)`: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so, 0x0006): Symbol not found: _R_getRegisteredNamespace
  Referenced from: <D5FEE207-EB8F-3FC2-BC24-84E97E708ECA> /Library/Frameworks/R.framework/Versions/4.6/Resources/library/igraph/libs/igraph.so
  Expected in:     <9885FFC9-0B1B-386C-8515-0CC182A63B5A> /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib
Backtrace:
    ▆
 1. └─base::loadNamespace(x) at test-clusterGraph.R:34:5
 2.   └─base::library.dynam(lib, package, package.lib)
 3.     └─base::dyn.load(file, DLLpath = DLLpath, ...)
── Error ('test-normalizeCounts.R:12:5'): normalizeCounts gives the same results in all modes ──
Error in `eval_bare(expr, quo_get_env(quo))`: object 'tatami_row' not found
Backtrace:
    ▆
 1. └─testthat::expect_equal(y[1, ], beachmat:::tatami_row(z, 1)) at test-normalizeCounts.R:12:5
 2.   └─testthat::quasi_label(enquo(expected), expected.label)
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1317 ]
Error:
! Test failures.
Execution halted

Example timings

scrapper.Rcheck/scrapper-Ex.timings

name	user	system	elapsed
LogNormalizedMatrix	0.040	0.001	0.041
adt_quality_control	0.085	0.001	0.087
aggregateAcrossCells	0.011	0.000	0.012
aggregateAcrossCells.se	6.471	0.158	6.676
aggregateAcrossGenes	0.009	0.000	0.009
aggregateAcrossGenes.se	1.178	0.092	1.283
analyze	0.984	0.063	3.246
analyze.se	3.484	0.071	7.143