Aaron Lun
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/scrapper |
| git_branch: devel |
| git_last_commit: 0f251ee |
| git_last_commit_date: 2025-01-06 13:31:50 -0500 (Mon, 06 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:40 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 1886/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.1.12 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.1.12 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scrapper_1.1.12.tar.gz |
| StartedAt: 2025-01-11 02:08:04 -0500 (Sat, 11 Jan 2025) |
| EndedAt: 2025-01-11 02:15:00 -0500 (Sat, 11 Jan 2025) |
| EllapsedTime: 415.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scrapper.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scrapper_1.1.12.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scrapper.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.1.12’
* 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 installed package size ... INFO
installed size is 51.8Mb
sub-directories of 1Mb or more:
libs 51.5Mb
* 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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
analyze 16.395 0.819 22.414
runAllNeighborSteps 0.113 0.001 5.023
* 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 NOTE
See
‘/home/biocbuild/bbs-3.21-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-3.21-bioc/R/bin/R CMD INSTALL scrapper
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘scrapper’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c adt_quality_control.cpp -o adt_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c aggregate_across_cells.cpp -o aggregate_across_cells.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c aggregate_across_genes.cpp -o aggregate_across_genes.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c build_snn_graph.cpp -o build_snn_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c center_size_factors.cpp -o center_size_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c choose_pseudo_count.cpp -o choose_pseudo_count.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c cluster_graph.cpp -o cluster_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c cluster_kmeans.cpp -o cluster_kmeans.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c combine_factors.cpp -o combine_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c correct_mnn.cpp -o correct_mnn.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c crispr_quality_control.cpp -o crispr_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c fit_variance_trend.cpp -o fit_variance_trend.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c model_gene_variances.cpp -o model_gene_variances.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c normalize_counts.cpp -o normalize_counts.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c rna_quality_control.cpp -o rna_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c run_pca.cpp -o run_pca.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c run_tsne.cpp -o run_tsne.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c run_umap.cpp -o run_umap.o
In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/Eigen/Core:341,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/irlba/compute.hpp:4,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/irlba/irlba.hpp:4,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/umappp/spectral_init.hpp:4,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/umappp/initialize.hpp:8,
from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/umappp/umappp.hpp:11,
from run_umap.cpp:4:
/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c sanitize_size_factors.cpp -o sanitize_size_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c scale_by_neighbors.cpp -o scale_by_neighbors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c score_gene_set.cpp -o score_gene_set.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c score_markers.cpp -o score_markers.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c summarize_effects.cpp -o summarize_effects.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c test_enrichment.cpp -o test_enrichment.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-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 subsample_by_neighbors.o summarize_effects.o test_enrichment.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 780 ]
>
> proc.time()
user system elapsed
43.378 3.068 124.151
scrapper.Rcheck/scrapper-Ex.timings
| name | user | system | elapsed | |
| adt_quality_control | 0.044 | 0.002 | 0.046 | |
| aggregateAcrossCells | 0.025 | 0.000 | 0.025 | |
| aggregateAcrossGenes | 0.015 | 0.000 | 0.016 | |
| analyze | 16.395 | 0.819 | 22.414 | |
| buildSnnGraph | 0.222 | 0.023 | 0.246 | |
| centerSizeFactors | 0.000 | 0.002 | 0.002 | |
| chooseHighlyVariableGenes | 0.001 | 0.000 | 0.002 | |
| choosePseudoCount | 0.000 | 0.000 | 0.001 | |
| clusterGraph | 0.842 | 0.044 | 0.887 | |
| clusterKmeans | 0.001 | 0.001 | 0.003 | |
| combineFactors | 0.002 | 0.003 | 0.005 | |
| computeClrm1Factors | 0.024 | 0.003 | 0.026 | |
| correctMnn | 0.415 | 0.000 | 0.414 | |
| crispr_quality_control | 0.017 | 0.003 | 0.019 | |
| fitVarianceTrend | 0.018 | 0.000 | 0.017 | |
| modelGeneVariances | 0.048 | 0.005 | 0.053 | |
| normalizeCounts | 0.118 | 0.024 | 0.143 | |
| rna_quality_control | 0.023 | 0.004 | 0.027 | |
| runAllNeighborSteps | 0.113 | 0.001 | 5.023 | |
| runPca | 0.116 | 0.007 | 0.123 | |
| runTsne | 0.229 | 0.001 | 0.230 | |
| runUmap | 0.179 | 0.001 | 0.180 | |
| sanitizeSizeFactors | 0.000 | 0.001 | 0.002 | |
| scaleByNeighbors | 0.112 | 0.003 | 0.115 | |
| scoreGeneSet | 0.052 | 0.012 | 0.064 | |
| scoreMarkers | 0.127 | 0.153 | 0.279 | |
| subsampleByNeighbors | 1.491 | 0.026 | 1.518 | |
| summarizeEffects | 0.072 | 0.015 | 0.086 | |
| testEnrichment | 0.000 | 0.001 | 0.001 | |