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This page was generated on 2026-05-07 16:13 -0400 (Thu, 07 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-22 r89945) -- "Because it was There" 923
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Package 196/231HostnameOS / ArchINSTALLBUILDCHECKBIOCCHECK
scrapper 1.6.2  (landing page)
Aaron Lun
Snapshot Date: 2026-05-07 13:01 -0400 (Thu, 07 May 2026)
git_url: https://git.bioconductor.org/packages/scrapper
git_branch: RELEASE_3_23
git_last_commit: 93b85f2
git_last_commit_date: 2026-05-03 23:45:20 -0400 (Sun, 03 May 2026)
teran2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    WARNINGS    TIMEOUT  

CHECK results for scrapper on teran2

To the developers/maintainers of the scrapper package:
- 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: 1.6.2
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings scrapper_1.6.2.tar.gz
StartedAt: 2026-05-07 14:55:01 -0400 (Thu, 07 May 2026)
EndedAt: 2026-05-07 15:01:18 -0400 (Thu, 07 May 2026)
EllapsedTime: 376.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scrapper.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings scrapper_1.6.2.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/scrapper.Rcheck’
* using R version 4.6.0 RC (2026-04-22 r89945)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-07 18:55:02 UTC
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.6.2’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... INFO
  installed size is 114.8Mb
  sub-directories of 1Mb or more:
    libs  114.1Mb
* 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 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 ... 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 ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/scrapper/libs/scrapper.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
aggregateAcrossCells.se 14.045  0.715  14.842
getTestData.se           7.967  0.611   8.746
analyze.se               6.176  0.261  10.855
analyze                  1.462  0.132   5.361
runAllNeighborSteps.se   1.093  0.007   5.256
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/scrapper.Rcheck/00check.log’
for details.

Installation output

scrapper.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL scrapper
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘scrapper’ ...
** this is package ‘scrapper’ version ‘1.6.2’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c adt_quality_control.cpp -o adt_quality_control.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c aggregate_across_cells.cpp -o aggregate_across_cells.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c aggregate_across_genes.cpp -o aggregate_across_genes.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c build_snn_graph.cpp -o build_snn_graph.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c center_size_factors.cpp -o center_size_factors.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c choose_pseudo_count.cpp -o choose_pseudo_count.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c cluster_graph.cpp -o cluster_graph.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c cluster_kmeans.cpp -o cluster_kmeans.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c combine_factors.cpp -o combine_factors.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c compute_block_weights.cpp -o compute_block_weights.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c correct_mnn.cpp -o correct_mnn.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c crispr_quality_control.cpp -o crispr_quality_control.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fit_variance_trend.cpp -o fit_variance_trend.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c model_gene_variances.cpp -o model_gene_variances.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c normalize_counts.cpp -o normalize_counts.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rna_quality_control.cpp -o rna_quality_control.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c run_pca.cpp -o run_pca.o
run_pca.cpp: In function ‘Rcpp::List run_pca(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, Rcpp::Nullable<Rcpp::Vector<13> >, bool, Rcpp::Nullable<Rcpp::Vector<13> >, int, double, double, int)’:
run_pca.cpp:97:48: warning: alias template deduction only available with ‘-std=c++20’ or ‘-std=gnu++20’
   97 |             scran_pca::SubsetPcaBlockedOptions opt;
      |                                                ^~~
run_pca.cpp:97:48: note: use ‘template<class EigenVector_> struct scran_pca::BlockedPcaOptions’ directly instead
run_pca.cpp:110:41: warning: alias template deduction only available with ‘-std=c++20’ or ‘-std=gnu++20’
  110 |             scran_pca::SubsetPcaOptions opt;
      |                                         ^~~
run_pca.cpp:110:41: note: use ‘template<class EigenVector_> struct scran_pca::SimplePcaOptions’ directly instead
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c run_tsne.cpp -o run_tsne.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c run_umap.cpp -o run_umap.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c sanitize_size_factors.cpp -o sanitize_size_factors.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c scale_by_neighbors.cpp -o scale_by_neighbors.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c score_gene_set.cpp -o score_gene_set.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c score_markers.cpp -o score_markers.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c set_executor.cpp -o set_executor.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c summarize_effects.cpp -o summarize_effects.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BiocNeighbors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test_enrichment.cpp -o test_enrichment.o
g++ -std=gnu++17 -shared -L/usr/local/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 /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rigraphlib/igraph/lib/libigraph.a -llapack -L/home/rapidbuild/bbs-3.23-bioc-rapid/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-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


R version 4.6.0 RC (2026-04-22 r89945) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1357 ]
> 
> proc.time()
   user  system elapsed 
 33.183   0.884 112.613

Example timings

scrapper.Rcheck/scrapper-Ex.timings

nameusersystemelapsed
LogNormalizedMatrix0.0810.0030.083
adt_quality_control0.2030.0010.205
aggregateAcrossCells0.0250.0020.027
aggregateAcrossCells.se14.045 0.71514.842
aggregateAcrossGenes0.0170.0020.019
aggregateAcrossGenes.se2.2160.1642.441
analyze1.4620.1325.361
analyze.se 6.176 0.26110.855
buildSnnGraph0.1700.0040.174
centerSizeFactors0.0010.0000.001
chooseHighlyVariableGenes0.0010.0000.001
choosePseudoCount0.0010.0000.000
chooseRnaHvgs.se0.4230.0080.431
clusterGraph0.6580.0140.672
clusterGraph.se1.4060.0791.486
clusterKmeans0.0010.0000.002
clusterKmeans.se0.0220.0000.022
combineFactors0.0120.0000.013
computeBlockWeights0.0010.0000.000
computeClrm1Factors0.0140.0000.014
correctMnn0.3610.0000.361
correctMnn.se0.7650.0050.772
countGroupsByBlock0.0020.0000.002
crispr_quality_control0.0190.0000.019
fitVarianceTrend0.3460.0030.350
getTestData.se7.9670.6118.746
modelGeneVariances0.0570.0010.058
normalizeAdtCounts.se0.2950.0030.299
normalizeCounts0.0250.0000.025
normalizeCrisprCounts.se1.6430.2041.847
normalizeRnaCounts.se0.1340.0020.136
quickAdtQc.se0.1270.0070.134
quickCrisprQc.se0.1190.0020.121
quickRnaQc.se0.3110.0040.315
rna_quality_control0.0350.0000.035
runAllNeighborSteps0.0880.0053.915
runAllNeighborSteps.se1.0930.0075.256
runPca0.0490.0020.054
runPca.se0.9440.0270.972
runTsne0.1240.0000.123
runTsne.se1.2690.0041.274
runUmap0.1380.0000.138
runUmap.se0.7210.0030.725
sanitizeSizeFactors0.0010.0000.001
scaleByNeighbors0.0780.0000.079
scaleByNeighbors.se2.2510.0042.257
scoreGeneSet0.0180.0000.018
scoreGeneSet.se0.6050.0410.646
scoreMarkers0.1790.0330.212
scoreMarkers.se3.9920.0354.030
subsampleByNeighbors1.0330.0031.035
summarizeEffects0.0520.0020.053
testEnrichment0.0040.0000.004