Aaron Lun
| Snapshot Date: 2026-02-20 13:40 -0500 (Fri, 20 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) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-21 11:32 -0500 (Sat, 21 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4871 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1946/2354 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.5.12 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| See other builds for scrapper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the scrapper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scrapper.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: scrapper |
| Version: 1.5.12 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings scrapper_1.5.12.tar.gz |
| StartedAt: 2026-02-21 03:52:18 -0500 (Sat, 21 Feb 2026) |
| EndedAt: 2026-02-21 04:00:45 -0500 (Sat, 21 Feb 2026) |
| EllapsedTime: 507.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scrapper.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings scrapper_1.5.12.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/scrapper.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 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 37.4Mb
sub-directories of 1Mb or more:
libs 36.7Mb
* 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 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 ‘/home/biocbuild/bbs-3.23-bioc/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 15.510 0.730 16.241
getTestData.se 8.255 1.197 9.756
analyze.se 8.041 0.447 14.568
scoreMarkers.se 5.192 0.312 5.505
analyze 2.274 0.170 7.354
runAllNeighborSteps.se 1.545 0.049 7.039
runAllNeighborSteps 0.082 0.020 5.220
* 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
‘/home/biocbuild/bbs-3.23-bioc/meat/scrapper.Rcheck/00check.log’
for details.
scrapper.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL scrapper
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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 /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/Core:335,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/utils.hpp:9,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/compute.hpp:10,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/irlba.hpp:4,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/gsdecon/compute.hpp:8,
from /home/biocbuild/bbs-3.23-bioc/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 /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:541:7,
inlined from ‘Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >::~PlainObjectBase()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7,
inlined from ‘Eigen::Matrix<double, -1, 1>::~Matrix()’ at /home/biocbuild/bbs-3.23-bioc/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 /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/Options.hpp:20:8,
inlined from ‘gsdecon::Options::~Options()’ at /home/biocbuild/bbs-3.23-bioc/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:
/home/biocbuild/bbs-3.23-bioc/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 /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:541:7,
inlined from ‘Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >::~PlainObjectBase()’ at /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7,
inlined from ‘Eigen::Matrix<double, -1, 1>::~Matrix()’ at /home/biocbuild/bbs-3.23-bioc/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 /home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include/irlba/Options.hpp:20:8,
inlined from ‘gsdecon::Options::~Options()’ at /home/biocbuild/bbs-3.23-bioc/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:
/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BiocNeighbors/include' -I'/home/biocbuild/bbs-3.23-bioc/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/home/biocbuild/bbs-3.23-bioc/R/lib -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 /home/biocbuild/bbs-3.23-bioc/R/site-library/Rigraphlib/igraph/lib/libigraph.a -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/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)
scrapper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
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.
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Type 'contributors()' for more information and
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> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1316 ]
>
> proc.time()
user system elapsed
47.731 2.535 155.167
scrapper.Rcheck/scrapper-Ex.timings
| name | user | system | elapsed | |
| LogNormalizedMatrix | 0.119 | 0.003 | 0.122 | |
| adt_quality_control | 0.212 | 0.001 | 0.214 | |
| aggregateAcrossCells | 0.038 | 0.003 | 0.041 | |
| aggregateAcrossCells.se | 15.510 | 0.730 | 16.241 | |
| aggregateAcrossGenes | 0.024 | 0.003 | 0.026 | |
| aggregateAcrossGenes.se | 2.608 | 0.220 | 2.910 | |
| analyze | 2.274 | 0.170 | 7.354 | |
| analyze.se | 8.041 | 0.447 | 14.568 | |
| buildSnnGraph | 0.220 | 0.016 | 0.237 | |
| centerSizeFactors | 0.000 | 0.002 | 0.002 | |
| chooseHighlyVariableGenes | 0.002 | 0.000 | 0.001 | |
| choosePseudoCount | 0.001 | 0.001 | 0.000 | |
| chooseRnaHvgs.se | 0.662 | 0.076 | 0.738 | |
| clusterGraph | 0.874 | 0.029 | 0.904 | |
| clusterGraph.se | 1.893 | 0.091 | 1.987 | |
| clusterKmeans | 0.002 | 0.000 | 0.003 | |
| clusterKmeans.se | 0.032 | 0.002 | 0.034 | |
| combineFactors | 0.017 | 0.003 | 0.020 | |
| computeBlockWeights | 0.000 | 0.001 | 0.001 | |
| computeClrm1Factors | 0.021 | 0.010 | 0.031 | |
| correctMnn | 0.484 | 0.001 | 0.485 | |
| correctMnn.se | 1.060 | 0.093 | 1.154 | |
| countGroupsByBlock | 0.005 | 0.000 | 0.005 | |
| crispr_quality_control | 0.030 | 0.006 | 0.036 | |
| fitVarianceTrend | 0.431 | 0.009 | 0.440 | |
| getTestData.se | 8.255 | 1.197 | 9.756 | |
| modelGeneVariances | 0.086 | 0.003 | 0.089 | |
| normalizeAdtCounts.se | 0.407 | 0.034 | 0.441 | |
| normalizeCounts | 0.035 | 0.000 | 0.035 | |
| normalizeCrisprCounts.se | 1.953 | 0.355 | 2.308 | |
| normalizeRnaCounts.se | 0.251 | 0.013 | 0.264 | |
| quickAdtQc.se | 0.233 | 0.017 | 0.250 | |
| quickCrisprQc.se | 0.193 | 0.010 | 0.203 | |
| quickRnaQc.se | 0.463 | 0.048 | 0.512 | |
| rna_quality_control | 0.050 | 0.001 | 0.050 | |
| runAllNeighborSteps | 0.082 | 0.020 | 5.220 | |
| runAllNeighborSteps.se | 1.545 | 0.049 | 7.039 | |
| runPca | 0.101 | 0.008 | 0.109 | |
| runPca.se | 1.425 | 0.209 | 1.636 | |
| runTsne | 0.184 | 0.008 | 0.192 | |
| runTsne.se | 1.825 | 0.072 | 1.896 | |
| runUmap | 0.189 | 0.002 | 0.192 | |
| runUmap.se | 1.057 | 0.040 | 1.097 | |
| sanitizeSizeFactors | 0.000 | 0.001 | 0.001 | |
| scaleByNeighbors | 0.11 | 0.00 | 0.11 | |
| scaleByNeighbors.se | 3.555 | 0.095 | 3.651 | |
| scoreGeneSet | 0.029 | 0.017 | 0.045 | |
| scoreGeneSet.se | 0.889 | 0.100 | 0.989 | |
| scoreMarkers | 0.256 | 0.174 | 0.430 | |
| scoreMarkers.se | 5.192 | 0.312 | 5.505 | |
| subsampleByNeighbors | 1.468 | 0.030 | 1.498 | |
| summarizeEffects | 0.076 | 0.011 | 0.087 | |
| testEnrichment | 0.006 | 0.001 | 0.007 | |