Aaron Lun
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/scrapper |
| git_branch: devel |
| git_last_commit: 8d77b42 |
| git_last_commit_date: 2025-06-04 11:22:57 -0400 (Wed, 04 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:02 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 1908/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.3.4 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.3.4 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scrapper_1.3.4.tar.gz |
| StartedAt: 2025-06-19 03:14:05 -0400 (Thu, 19 Jun 2025) |
| EndedAt: 2025-06-19 03:21:08 -0400 (Thu, 19 Jun 2025) |
| EllapsedTime: 423.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scrapper.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scrapper_1.3.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/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 ‘1.3.4’
* 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 113.8Mb
sub-directories of 1Mb or more:
libs 113.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ‘/home/biocbuild/bbs-3.22-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
analyze 17.550 0.850 23.556
runAllNeighborSteps 0.109 0.008 5.233
* 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-3.22-bioc/meat/scrapper.Rcheck/00check.log’
for details.
scrapper.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scrapper
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scrapper’ ...
** this is package ‘scrapper’ version ‘1.3.4’
** 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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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 /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/Eigen/Core:341,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/irlba/compute.hpp:4,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/irlba/irlba.hpp:4,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/umappp/spectral_init.hpp:4,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/umappp/initialize.hpp:8,
from /home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include/umappp/umappp.hpp:11,
from run_umap.cpp:4:
/home/biocbuild/bbs-3.22-bioc/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]’:
/home/biocbuild/bbs-3.22-bioc/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);
| ~~~~~~~~~~~~
/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rigraphlib/igraph/include/igraph' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.22-bioc/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/home/biocbuild/bbs-3.22-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_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-3.22-bioc/R/site-library/Rigraphlib/igraph/lib/libigraph.a -llapack -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 796 ]
>
> proc.time()
user system elapsed
46.421 3.097 126.593
scrapper.Rcheck/scrapper-Ex.timings
| name | user | system | elapsed | |
| adt_quality_control | 0.060 | 0.002 | 0.063 | |
| aggregateAcrossCells | 0.026 | 0.001 | 0.027 | |
| aggregateAcrossGenes | 0.016 | 0.000 | 0.017 | |
| analyze | 17.550 | 0.850 | 23.556 | |
| buildSnnGraph | 0.226 | 0.035 | 0.262 | |
| centerSizeFactors | 0.000 | 0.000 | 0.001 | |
| chooseHighlyVariableGenes | 0.001 | 0.001 | 0.002 | |
| choosePseudoCount | 0 | 0 | 0 | |
| clusterGraph | 0.831 | 0.076 | 0.908 | |
| clusterKmeans | 0.002 | 0.001 | 0.002 | |
| combineFactors | 0.002 | 0.004 | 0.005 | |
| computeClrm1Factors | 0.029 | 0.023 | 0.052 | |
| correctMnn | 0.479 | 0.003 | 0.481 | |
| crispr_quality_control | 0.024 | 0.004 | 0.027 | |
| fitVarianceTrend | 0.017 | 0.016 | 0.032 | |
| modelGeneVariances | 0.048 | 0.049 | 0.096 | |
| normalizeCounts | 0.096 | 0.040 | 0.136 | |
| rna_quality_control | 0.027 | 0.003 | 0.030 | |
| runAllNeighborSteps | 0.109 | 0.008 | 5.233 | |
| runPca | 0.128 | 0.008 | 0.137 | |
| runTsne | 0.218 | 0.009 | 0.227 | |
| runUmap | 0.176 | 0.002 | 0.179 | |
| sanitizeSizeFactors | 0.001 | 0.000 | 0.001 | |
| scaleByNeighbors | 0.110 | 0.007 | 0.117 | |
| scoreGeneSet | 0.059 | 0.047 | 0.105 | |
| scoreMarkers | 0.126 | 0.037 | 0.163 | |
| subsampleByNeighbors | 1.466 | 0.102 | 1.567 | |
| summarizeEffects | 0.070 | 0.014 | 0.084 | |
| testEnrichment | 0.001 | 0.000 | 0.001 | |