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This page was generated on 2025-07-24 09:37 -0400 (Thu, 24 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 914
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Package 195/229HostnameOS / ArchINSTALLBUILDCHECK
scrapper 1.3.5  (landing page)
Aaron Lun
Snapshot Date: 2025-07-24 06:00 -0400 (Thu, 24 Jul 2025)
git_url: https://git.bioconductor.org/packages/scrapper
git_branch: devel
git_last_commit: 3924f5b
git_last_commit_date: 2025-07-14 02:16:08 -0400 (Mon, 14 Jul 2025)
teran2Linux (Ubuntu 24.04.1 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: 1.3.5
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings scrapper_1.3.5.tar.gz
StartedAt: 2025-07-24 08:57:59 -0400 (Thu, 24 Jul 2025)
EndedAt: 2025-07-24 09:03:14 -0400 (Thu, 24 Jul 2025)
EllapsedTime: 314.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scrapper.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings scrapper_1.3.5.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/scrapper.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.3.5’
* 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) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is 111.4Mb
  sub-directories of 1Mb or more:
    libs  111.1Mb
* 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
* 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 ... NOTE
Namespace in Imports field not imported from: ‘Rigraphlib’
  All declared Imports should be used.
* 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-3.22-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
analyze 18.113  0.986  23.036
* 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, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/scrapper.Rcheck/00check.log’
for details.

Installation output

scrapper.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL scrapper
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘scrapper’ ...
** this is package ‘scrapper’ version ‘1.3.5’
** using staged installation
** libs
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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c run_umap.cpp -o run_umap.o
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/Eigen/Core:341,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/Eigen/Dense:1,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/irlba/compute.hpp:4,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/irlba/irlba.hpp:4,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/umappp/spectral_init.hpp:4,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/umappp/initialize.hpp:8,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/umappp/umappp.hpp:11,
                 from run_umap.cpp:4:
/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’:
/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
  327 |     internal::triangular_matrix_vector_product
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  328 |       <Index,Mode,
      |       ~~~~~~~~~~~~
  329 |        LhsScalar, LhsBlasTraits::NeedToConjugate,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  330 |        RhsScalar, RhsBlasTraits::NeedToConjugate,
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  331 |        RowMajor>
      |        ~~~~~~~~~
  332 |       ::run(actualLhs.rows(),actualLhs.cols(),
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  333 |             actualLhs.data(),actualLhs.outerStride(),
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  334 |             actualRhsPtr,1,
      |             ~~~~~~~~~~~~~~~
  335 |             dest.data(),dest.innerStride(),
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  336 |             actualAlpha);
      |             ~~~~~~~~~~~~
/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here
  105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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-3.22-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/include/igraph' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library/BiocNeighbors/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_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-3.22-bioc-rapid/R/site-library/Rigraphlib/igraph/lib/libigraph.a -llapack -L/home/rapidbuild/bbs-3.22-bioc-rapid/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.22-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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
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> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 796 ]
> 
> proc.time()
   user  system elapsed 
 34.502   1.503  91.161

Example timings

scrapper.Rcheck/scrapper-Ex.timings

nameusersystemelapsed
adt_quality_control0.0540.0020.057
aggregateAcrossCells0.0230.0000.030
aggregateAcrossGenes0.0110.0010.012
analyze18.113 0.98623.036
buildSnnGraph0.1610.0150.176
centerSizeFactors0.0010.0000.001
chooseHighlyVariableGenes0.0010.0000.001
choosePseudoCount0.0010.0000.000
clusterGraph0.6000.0140.614
clusterKmeans0.0020.0000.001
combineFactors0.0030.0000.002
computeClrm1Factors0.0190.0000.021
correctMnn0.3580.0010.358
crispr_quality_control0.0110.0010.011
fitVarianceTrend0.0100.0000.009
modelGeneVariances0.0310.0000.031
normalizeCounts0.0530.0010.054
rna_quality_control0.0170.0000.017
runAllNeighborSteps0.0840.0044.191
runPca0.0830.0040.087
runTsne0.1520.0040.156
runUmap0.1280.0010.129
sanitizeSizeFactors0.0010.0000.001
scaleByNeighbors0.0780.0010.079
scoreGeneSet0.0360.0090.046
scoreMarkers0.0860.0470.133
subsampleByNeighbors1.0450.0081.053
summarizeEffects0.0470.0010.048
testEnrichment0.0000.0010.000