Aaron Lun
| Snapshot Date: 2024-11-04 13:40 -0500 (Mon, 04 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/scrapper |
| git_branch: RELEASE_3_20 |
| git_last_commit: b0d67cf |
| git_last_commit_date: 2024-10-29 11:33:53 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-05 12:03 -0500 (Tue, 05 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4503 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 1898/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.0.0 (landing page) Aaron Lun
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | 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: 1.0.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scrapper_1.0.0.tar.gz |
| StartedAt: 2024-11-05 07:32:16 -0500 (Tue, 05 Nov 2024) |
| EndedAt: 2024-11-05 07:36:03 -0500 (Tue, 05 Nov 2024) |
| EllapsedTime: 226.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scrapper.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scrapper_1.0.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/scrapper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.0.0’
* 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 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... NOTE
installed size is 105.7Mb
sub-directories of 1Mb or more:
libs 105.5Mb
* 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
* 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: 2 NOTEs
See
‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/scrapper.Rcheck/00check.log’
for details.
scrapper.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scrapper
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘scrapper’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c adt_quality_control.cpp -o adt_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c aggregate_across_cells.cpp -o aggregate_across_cells.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c build_snn_graph.cpp -o build_snn_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c center_size_factors.cpp -o center_size_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c choose_pseudo_count.cpp -o choose_pseudo_count.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c cluster_graph.cpp -o cluster_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c cluster_kmeans.cpp -o cluster_kmeans.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c combine_factors.cpp -o combine_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c correct_mnn.cpp -o correct_mnn.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c crispr_quality_control.cpp -o crispr_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c fit_variance_trend.cpp -o fit_variance_trend.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c model_gene_variances.cpp -o model_gene_variances.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c normalize_counts.cpp -o normalize_counts.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c rna_quality_control.cpp -o rna_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c run_pca.cpp -o run_pca.o
In file included from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/Eigen/Core:341,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/Eigen/Dense:1,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/irlba/irlba.hpp:4,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/scran_pca/simple_pca.hpp:6,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/scran_pca/scran_pca.hpp:4,
from run_pca.cpp:10:
/media/volume/teran2_disk/biocbuild/bbs-3.20-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]’:
/media/volume/teran2_disk/biocbuild/bbs-3.20-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);
| ~~~~~~~~~~~~
/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c run_tsne.cpp -o run_tsne.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c run_umap.cpp -o run_umap.o
In file included from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/Eigen/Core:341,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/Eigen/Dense:1,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/irlba/irlba.hpp:4,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/umappp/spectral_init.hpp:4,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/umappp/initialize.hpp:8,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/umappp/umappp.hpp:11,
from run_umap.cpp:4:
/media/volume/teran2_disk/biocbuild/bbs-3.20-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]’:
/media/volume/teran2_disk/biocbuild/bbs-3.20-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);
| ~~~~~~~~~~~~
/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c sanitize_size_factors.cpp -o sanitize_size_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c scale_by_neighbors.cpp -o scale_by_neighbors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c score_gene_set.cpp -o score_gene_set.o
In file included from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/Eigen/Core:341,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/Eigen/Dense:1,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/irlba/irlba.hpp:4,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/gsdecon/compute.hpp:8,
from /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include/gsdecon/gsdecon.hpp:4,
from score_gene_set.cpp:7:
/media/volume/teran2_disk/biocbuild/bbs-3.20-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]’:
/media/volume/teran2_disk/biocbuild/bbs-3.20-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);
| ~~~~~~~~~~~~
/media/volume/teran2_disk/biocbuild/bbs-3.20-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-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c score_markers.cpp -o score_markers.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c summarize_effects.cpp -o summarize_effects.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.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 -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-scrapper/00new/scrapper/libs
** R
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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 642 ]
>
> proc.time()
user system elapsed
10.907 0.494 38.274
scrapper.Rcheck/scrapper-Ex.timings
| name | user | system | elapsed | |
| adt_quality_control | 0.043 | 0.000 | 0.043 | |
| aggregateAcrossCells | 0.017 | 0.001 | 0.018 | |
| buildSnnGraph | 0.393 | 0.011 | 0.405 | |
| centerSizeFactors | 0.001 | 0.000 | 0.001 | |
| chooseHighlyVariableGenes | 0.001 | 0.000 | 0.001 | |
| choosePseudoCount | 0 | 0 | 0 | |
| clusterGraph | 1.039 | 0.005 | 1.072 | |
| clusterKmeans | 0.002 | 0.000 | 0.002 | |
| combineFactors | 0.003 | 0.000 | 0.003 | |
| computeClrm1Factors | 0.011 | 0.000 | 0.011 | |
| correctMnn | 0.298 | 0.000 | 0.299 | |
| crispr_quality_control | 0.008 | 0.000 | 0.009 | |
| fitVarianceTrend | 0.008 | 0.001 | 0.010 | |
| modelGeneVariances | 0.025 | 0.002 | 0.027 | |
| normalizeCounts | 0.078 | 0.001 | 0.079 | |
| rna_quality_control | 0.013 | 0.001 | 0.014 | |
| runAllNeighborSteps | 0.092 | 0.006 | 4.930 | |
| runPca | 0.074 | 0.005 | 0.163 | |
| runTsne | 0.156 | 0.000 | 0.157 | |
| runUmap | 0.128 | 0.000 | 0.128 | |
| sanitizeSizeFactors | 0.001 | 0.000 | 0.003 | |
| scaleByNeighbors | 0.078 | 0.000 | 0.078 | |
| scoreGeneSet | 0.034 | 0.006 | 0.044 | |
| scoreMarkers | 0.046 | 0.010 | 0.058 | |
| subsampleByNeighbors | 1.018 | 0.003 | 1.127 | |
| summarizeEffects | 0.052 | 0.002 | 0.054 | |