Aaron Lun
| Snapshot Date: 2026-01-05 13:40 -0500 (Mon, 05 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/scrapper |
| git_branch: devel |
| git_last_commit: 94857a9 |
| git_last_commit_date: 2026-01-04 21:26:16 -0500 (Sun, 04 Jan 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-06 11:35 -0500 (Tue, 06 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1927/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.5.7 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 1.5.7 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scrapper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scrapper_1.5.7.tar.gz |
| StartedAt: 2026-01-05 22:19:06 -0500 (Mon, 05 Jan 2026) |
| EndedAt: 2026-01-05 22:22:03 -0500 (Mon, 05 Jan 2026) |
| EllapsedTime: 177.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scrapper.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scrapper.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scrapper_1.5.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/scrapper.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.5.7’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scrapper’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘assorthead’ is only usable in R >= 3.0.2
'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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/scrapper/libs/scrapper.so’:
Found ‘___assert_rtn’, possibly from ‘assert’ (C)
Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘___stderrp’, possibly from ‘stderr’ (C)
Found ‘___stdoutp’, possibly from ‘stdout’ (C)
Found ‘_abort’, possibly from ‘abort’ (C)
Found ‘_printf’, possibly from ‘printf’ (C)
Found ‘_putchar’, possibly from ‘putchar’ (C)
Found ‘_sprintf’, possibly from ‘sprintf’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
aggregateAcrossCells.se 7.038 0.184 7.584
analyze.se 4.320 0.064 8.343
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/scrapper.Rcheck/00check.log’
for details.
scrapper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scrapper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘scrapper’ ... ** this is package ‘scrapper’ version ‘1.5.7’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++17 using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c adt_quality_control.cpp -o adt_quality_control.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aggregate_across_cells.cpp -o aggregate_across_cells.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aggregate_across_genes.cpp -o aggregate_across_genes.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c build_snn_graph.cpp -o build_snn_graph.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c center_size_factors.cpp -o center_size_factors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c choose_pseudo_count.cpp -o choose_pseudo_count.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cluster_graph.cpp -o cluster_graph.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cluster_kmeans.cpp -o cluster_kmeans.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c combine_factors.cpp -o combine_factors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compute_block_weights.cpp -o compute_block_weights.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c correct_mnn.cpp -o correct_mnn.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c crispr_quality_control.cpp -o crispr_quality_control.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fit_variance_trend.cpp -o fit_variance_trend.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c model_gene_variances.cpp -o model_gene_variances.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c normalize_counts.cpp -o normalize_counts.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rna_quality_control.cpp -o rna_quality_control.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run_pca.cpp -o run_pca.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run_tsne.cpp -o run_tsne.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run_umap.cpp -o run_umap.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sanitize_size_factors.cpp -o sanitize_size_factors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scale_by_neighbors.cpp -o scale_by_neighbors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c score_gene_set.cpp -o score_gene_set.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c score_markers.cpp -o score_markers.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c set_executor.cpp -o set_executor.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c summarize_effects.cpp -o summarize_effects.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/include/igraph' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/BiocNeighbors/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test_enrichment.cpp -o test_enrichment.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.o aggregate_across_genes.o build_snn_graph.o center_size_factors.o choose_highly_variable_genes.o choose_pseudo_count.o cluster_graph.o cluster_kmeans.o combine_factors.o compute_block_weights.o compute_clrm1_factors.o correct_mnn.o crispr_quality_control.o fit_variance_trend.o model_gene_variances.o normalize_counts.o rna_quality_control.o run_pca.o run_tsne.o run_umap.o sanitize_size_factors.o scale_by_neighbors.o score_gene_set.o score_markers.o set_executor.o subsample_by_neighbors.o summarize_effects.o test_enrichment.o /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rigraphlib/igraph/lib/libigraph.a -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-scrapper/00new/scrapper/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scrapper)
scrapper.Rcheck/tests/testthat.Rout
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> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1265 ]
>
> proc.time()
user system elapsed
18.577 0.598 67.847
scrapper.Rcheck/scrapper-Ex.timings
| name | user | system | elapsed | |
| adt_quality_control | 0.045 | 0.001 | 0.047 | |
| aggregateAcrossCells | 0.012 | 0.001 | 0.012 | |
| aggregateAcrossCells.se | 7.038 | 0.184 | 7.584 | |
| aggregateAcrossGenes | 0.011 | 0.001 | 0.012 | |
| aggregateAcrossGenes.se | 1.429 | 0.091 | 1.602 | |
| analyze | 1.316 | 0.067 | 3.713 | |
| analyze.se | 4.320 | 0.064 | 8.343 | |
| buildSnnGraph | 0.116 | 0.002 | 0.128 | |
| centerSizeFactors | 0.000 | 0.001 | 0.001 | |
| chooseHighlyVariableGenes | 0.001 | 0.000 | 0.001 | |
| choosePseudoCount | 0 | 0 | 0 | |
| chooseRnaHvgs.se | 0.266 | 0.014 | 0.302 | |
| clusterGraph | 0.415 | 0.005 | 0.435 | |
| clusterGraph.se | 0.962 | 0.016 | 1.015 | |
| clusterKmeans | 0.000 | 0.000 | 0.001 | |
| clusterKmeans.se | 0.55 | 0.02 | 0.59 | |
| combineFactors | 0.006 | 0.001 | 0.007 | |
| computeBlockWeights | 0.000 | 0.000 | 0.001 | |
| computeClrm1Factors | 0.009 | 0.001 | 0.017 | |
| correctMnn | 0.275 | 0.002 | 0.288 | |
| correctMnn.se | 0.468 | 0.007 | 0.482 | |
| crispr_quality_control | 0.012 | 0.001 | 0.012 | |
| fitVarianceTrend | 0.259 | 0.003 | 0.264 | |
| getTestData.se | 3.398 | 0.193 | 3.817 | |
| modelGeneVariances | 0.028 | 0.001 | 0.030 | |
| normalizeAdtCounts.se | 0.162 | 0.009 | 0.176 | |
| normalizeCounts | 0.026 | 0.001 | 0.028 | |
| normalizeCrisprCounts.se | 0.782 | 0.040 | 0.883 | |
| normalizeRnaCounts.se | 0.230 | 0.006 | 0.242 | |
| quickAdtQc.se | 0.079 | 0.005 | 0.093 | |
| quickCrisprQc.se | 0.067 | 0.006 | 0.074 | |
| quickRnaQc.se | 0.184 | 0.006 | 0.203 | |
| rna_quality_control | 0.022 | 0.001 | 0.026 | |
| runAllNeighborSteps | 0.058 | 0.005 | 2.364 | |
| runAllNeighborSteps.se | 0.823 | 0.013 | 2.990 | |
| runPca | 0.046 | 0.003 | 0.051 | |
| runPca.se | 0.654 | 0.025 | 0.708 | |
| runTsne | 0.078 | 0.000 | 0.089 | |
| runTsne.se | 0.857 | 0.009 | 0.894 | |
| runUmap | 0.144 | 0.001 | 0.151 | |
| runUmap.se | 0.608 | 0.008 | 0.624 | |
| sanitizeSizeFactors | 0.000 | 0.000 | 0.001 | |
| scaleByNeighbors | 0.058 | 0.000 | 0.059 | |
| scaleByNeighbors.se | 1.760 | 0.036 | 1.887 | |
| scoreGeneSet | 0.020 | 0.000 | 0.021 | |
| scoreGeneSet.se | 0.506 | 0.068 | 0.611 | |
| scoreMarkers | 0.097 | 0.050 | 0.149 | |
| scoreMarkers.se | 2.274 | 0.016 | 2.397 | |
| subsampleByNeighbors | 0.837 | 0.004 | 0.854 | |
| summarizeEffects | 0.033 | 0.001 | 0.038 | |
| testEnrichment | 0.002 | 0.000 | 0.002 | |