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This page was generated on 2026-02-19 10:23 -0500 (Thu, 19 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-01-12 r89300) -- "Unsuffered Consequences" 927
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Package 196/230HostnameOS / ArchINSTALLBUILDCHECK
scrapper 1.5.12  (landing page)
Aaron Lun
Snapshot Date: 2026-02-19 06:00 -0500 (Thu, 19 Feb 2026)
git_url: https://git.bioconductor.org/packages/scrapper
git_branch: devel
git_last_commit: dd6b494
git_last_commit_date: 2026-02-11 19:01:52 -0500 (Wed, 11 Feb 2026)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  

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: 1.5.12
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_1.5.12.tar.gz
StartedAt: 2026-02-19 09:34:31 -0500 (Thu, 19 Feb 2026)
EndedAt: 2026-02-19 09:41:02 -0500 (Thu, 19 Feb 2026)
EllapsedTime: 391.0 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_1.5.12.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/scrapper.Rcheck’
* using R Under development (unstable) (2026-01-12 r89300)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.5.12’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’
* 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) 13.3.0’
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... INFO
  installed size is 75.2Mb
  sub-directories of 1Mb or more:
    libs  74.6Mb
* 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
'LinkingTo' for ‘Rigraphlib’ is unused as it has no 'include' directory
* 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 use of S3 registration ... 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 ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
aggregateAcrossCells.se 14.129  0.688  14.925
getTestData.se           8.252  0.593   9.516
analyze.se               6.275  0.245  10.742
analyze                  1.567  0.129   5.493
runAllNeighborSteps.se   1.088  0.006   5.318
* 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, 3 NOTEs
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 ‘1.5.12’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 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
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
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/Core:335,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/Dense:1,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/irlba/utils.hpp:9,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/irlba/compute.hpp:10,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/irlba/irlba.hpp:4,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/gsdecon/compute.hpp:8,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/gsdecon/gsdecon.hpp:4,
                 from score_gene_set.cpp:6:
In destructor ‘Eigen::internal::DenseStorage_impl<T, -1, -1, Cols, Options>::~DenseStorage_impl() [with T = double; int Cols = 1; int Options = 0]’,
    inlined from ‘Eigen::DenseStorage<double, -1, -1, 1, 0, true>::~DenseStorage()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:541:7,
    inlined from ‘Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >::~PlainObjectBase()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7,
    inlined from ‘Eigen::Matrix<double, -1, 1>::~Matrix()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/Matrix.h:186:7,
    inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_destroy() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /usr/include/c++/13/optional:287:35,
    inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /usr/include/c++/13/optional:318:14,
    inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /usr/include/c++/13/optional:315:7,
    inlined from ‘std::_Optional_payload<_Tp, false, _Copy, _Move>::~_Optional_payload() [with _Tp = Eigen::Matrix<double, -1, 1>; bool _Copy = false; bool _Move = false]’ at /usr/include/c++/13/optional:441:65,
    inlined from ‘std::_Optional_base<Eigen::Matrix<double, -1, 1>, false, false>::~_Optional_base()’ at /usr/include/c++/13/optional:512:12,
    inlined from ‘std::optional<Eigen::Matrix<double, -1, 1> >::~optional()’ at /usr/include/c++/13/optional:707:11,
    inlined from ‘irlba::Options<Eigen::Matrix<double, -1, 1> >::~Options()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/irlba/Options.hpp:20:8,
    inlined from ‘gsdecon::Options::~Options()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/gsdecon/Options.hpp:18:8,
    inlined from ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, int, int, double, int)’ at score_gene_set.cpp:64:1:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:368:85: warning: ‘*(Eigen::internal::DenseStorage_impl<double, -1, -1, 1, 0>*)((char*)&opt + offsetof(gsdecon::Options, gsdecon::Options::irlba_options.irlba::Options<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::initial.std::optional<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::<unnamed>.std::_Optional_base<Eigen::Matrix<double, -1, 1, 0, -1, 1>, false, false>::<unnamed>)).Eigen::internal::DenseStorage_impl<double, -1, -1, 1, 0>::m_data’ may be used uninitialized [-Wmaybe-uninitialized]
  368 |   EIGEN_DEVICE_FUNC ~DenseStorage_impl() { conditional_aligned_delete_auto<T, Align>(m_data, size()); }
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
score_gene_set.cpp: In function ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, int, int, double, int)’:
score_gene_set.cpp:31:22: note: ‘opt’ declared here
   31 |     gsdecon::Options opt;
      |                      ^~~
In destructor ‘Eigen::internal::DenseStorage_impl<T, -1, -1, Cols, Options>::~DenseStorage_impl() [with T = double; int Cols = 1; int Options = 0]’,
    inlined from ‘Eigen::DenseStorage<double, -1, -1, 1, 0, true>::~DenseStorage()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:541:7,
    inlined from ‘Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >::~PlainObjectBase()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7,
    inlined from ‘Eigen::Matrix<double, -1, 1>::~Matrix()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/Matrix.h:186:7,
    inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_destroy() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /usr/include/c++/13/optional:287:35,
    inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /usr/include/c++/13/optional:318:14,
    inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /usr/include/c++/13/optional:315:7,
    inlined from ‘std::_Optional_payload<_Tp, false, _Copy, _Move>::~_Optional_payload() [with _Tp = Eigen::Matrix<double, -1, 1>; bool _Copy = false; bool _Move = false]’ at /usr/include/c++/13/optional:441:65,
    inlined from ‘std::_Optional_base<Eigen::Matrix<double, -1, 1>, false, false>::~_Optional_base()’ at /usr/include/c++/13/optional:512:12,
    inlined from ‘std::optional<Eigen::Matrix<double, -1, 1> >::~optional()’ at /usr/include/c++/13/optional:707:11,
    inlined from ‘irlba::Options<Eigen::Matrix<double, -1, 1> >::~Options()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/irlba/Options.hpp:20:8,
    inlined from ‘gsdecon::Options::~Options()’ at /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/gsdecon/Options.hpp:18:8,
    inlined from ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, int, int, double, int)’ at score_gene_set.cpp:64:1:
/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:368:85: warning: ‘*(Eigen::internal::DenseStorage_impl<double, -1, -1, 1, 0>*)((char*)&opt + offsetof(gsdecon::Options, gsdecon::Options::irlba_options.irlba::Options<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::initial.std::optional<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::<unnamed>.std::_Optional_base<Eigen::Matrix<double, -1, 1, 0, -1, 1>, false, false>::<unnamed>)).Eigen::internal::DenseStorage_impl<double, -1, -1, 1, 0>::m_data’ may be used uninitialized [-Wmaybe-uninitialized]
  368 |   EIGEN_DEVICE_FUNC ~DenseStorage_impl() { conditional_aligned_delete_auto<T, Align>(m_data, size()); }
      |                                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
score_gene_set.cpp: In function ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, int, int, double, int)’:
score_gene_set.cpp:31:22: note: ‘opt’ declared here
   31 |     gsdecon::Options opt;
      |                      ^~~
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 Under development (unstable) (2026-01-12 r89300) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1316 ]
> 
> proc.time()
   user  system elapsed 
 34.451   0.782 114.443

Example timings

scrapper.Rcheck/scrapper-Ex.timings

nameusersystemelapsed
LogNormalizedMatrix0.0810.0020.083
adt_quality_control0.1960.0000.196
aggregateAcrossCells0.0240.0010.025
aggregateAcrossCells.se14.129 0.68814.925
aggregateAcrossGenes0.0190.0010.021
aggregateAcrossGenes.se2.3500.1562.525
analyze1.5670.1295.493
analyze.se 6.275 0.24510.742
buildSnnGraph0.1670.0010.169
centerSizeFactors0.0010.0000.001
chooseHighlyVariableGenes0.0000.0010.001
choosePseudoCount0.0010.0000.000
chooseRnaHvgs.se0.4150.0120.427
clusterGraph0.6660.0100.675
clusterGraph.se1.3620.0841.446
clusterKmeans0.0010.0000.002
clusterKmeans.se0.0220.0000.022
combineFactors0.0110.0010.012
computeBlockWeights0.0000.0000.001
computeClrm1Factors0.0140.0010.014
correctMnn0.3610.0010.362
correctMnn.se0.7690.0020.771
countGroupsByBlock0.0030.0000.003
crispr_quality_control0.0160.0030.020
fitVarianceTrend0.3450.0030.348
getTestData.se8.2520.5939.516
modelGeneVariances0.0580.0010.059
normalizeAdtCounts.se0.2670.0020.270
normalizeCounts0.0240.0020.026
normalizeCrisprCounts.se1.6460.2111.857
normalizeRnaCounts.se0.1300.0040.134
quickAdtQc.se0.1310.0030.134
quickCrisprQc.se0.1150.0040.120
quickRnaQc.se0.2920.0050.297
rna_quality_control0.0370.0010.038
runAllNeighborSteps0.0660.0033.861
runAllNeighborSteps.se1.0880.0065.318
runPca0.0590.0000.058
runPca.se0.8570.0250.883
runTsne0.1230.0000.124
runTsne.se1.2730.0041.278
runUmap0.1370.0000.137
runUmap.se0.7270.0040.731
sanitizeSizeFactors0.0000.0000.001
scaleByNeighbors0.0790.0000.079
scaleByNeighbors.se2.3690.0032.372
scoreGeneSet0.0180.0010.019
scoreGeneSet.se0.6200.0390.660
scoreMarkers0.1790.0310.210
scoreMarkers.se4.1360.0394.176
subsampleByNeighbors1.0470.0041.052
summarizeEffects0.0510.0040.055
testEnrichment0.0040.0000.004