Aaron Lun
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/scrapper |
| git_branch: devel |
| git_last_commit: 44598e5 |
| git_last_commit_date: 2024-11-18 12:09:49 -0500 (Mon, 18 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:39 -0500 (Mon, 25 Nov 2024).
| 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" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| 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 1881/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.1.4 (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 | | ||||||||
|
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: 1.1.4 |
| 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_1.1.4.tar.gz |
| StartedAt: 2024-11-25 02:05:27 -0500 (Mon, 25 Nov 2024) |
| EndedAt: 2024-11-25 02:11:35 -0500 (Mon, 25 Nov 2024) |
| EllapsedTime: 368.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scrapper.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.1.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scrapper.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.1.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
buildSnnGraph.Rd: buildIndex, BiocNeighborParam-class
correctMnn.Rd: BiocNeighborParam-class
normalizeCounts.Rd: initializeCpp, DelayedArray-class
runAllNeighborSteps.Rd: buildIndex, BiocNeighborParam-class
runTsne.Rd: buildIndex, BiocNeighborParam-class
runUmap.Rd: buildIndex, BiocNeighborParam-class
scaleByNeighbors.Rd: BiocNeighborParam-class
subsampleByNeighbors.Rd: buildIndex, BiocNeighborParam-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/scrapper.Rcheck/00check.log’
for details.
scrapper.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scrapper
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘scrapper’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c adt_quality_control.cpp -o adt_quality_control.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c aggregate_across_cells.cpp -o aggregate_across_cells.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c aggregate_across_genes.cpp -o aggregate_across_genes.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c build_snn_graph.cpp -o build_snn_graph.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c center_size_factors.cpp -o center_size_factors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c choose_pseudo_count.cpp -o choose_pseudo_count.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cluster_graph.cpp -o cluster_graph.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cluster_kmeans.cpp -o cluster_kmeans.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c combine_factors.cpp -o combine_factors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c correct_mnn.cpp -o correct_mnn.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c crispr_quality_control.cpp -o crispr_quality_control.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fit_variance_trend.cpp -o fit_variance_trend.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c model_gene_variances.cpp -o model_gene_variances.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c normalize_counts.cpp -o normalize_counts.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rna_quality_control.cpp -o rna_quality_control.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c run_pca.cpp -o run_pca.o
In file included from run_pca.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/scran_pca/scran_pca.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/scran_pca/simple_pca.hpp:7:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/irlba/parallel.hpp:444:9: warning: private field 'my_previous' is not used [-Wunused-private-field]
int my_previous;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c run_tsne.cpp -o run_tsne.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c run_umap.cpp -o run_umap.o
In file included from run_umap.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/umappp/umappp.hpp:11:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/umappp/initialize.hpp:8:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/umappp/spectral_init.hpp:5:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/irlba/parallel.hpp:444:9: warning: private field 'my_previous' is not used [-Wunused-private-field]
int my_previous;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sanitize_size_factors.cpp -o sanitize_size_factors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c scale_by_neighbors.cpp -o scale_by_neighbors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c score_gene_set.cpp -o score_gene_set.o
In file included from score_gene_set.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/gsdecon/gsdecon.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/gsdecon/compute.hpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/scran_pca/scran_pca.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/scran_pca/simple_pca.hpp:7:
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include/irlba/parallel.hpp:444:9: warning: private field 'my_previous' is not used [-Wunused-private-field]
int my_previous;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c score_markers.cpp -o score_markers.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BiocNeighbors/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c summarize_effects.cpp -o summarize_effects.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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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Platform: x86_64-apple-darwin20
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> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 676 ]
>
> proc.time()
user system elapsed
11.453 0.716 38.421
scrapper.Rcheck/scrapper-Ex.timings
| name | user | system | elapsed | |
| adt_quality_control | 0.040 | 0.002 | 0.043 | |
| aggregateAcrossCells | 0.021 | 0.002 | 0.023 | |
| aggregateAcrossGenes | 0.013 | 0.001 | 0.014 | |
| buildSnnGraph | 0.593 | 0.013 | 0.606 | |
| centerSizeFactors | 0.001 | 0.001 | 0.002 | |
| chooseHighlyVariableGenes | 0.001 | 0.001 | 0.002 | |
| choosePseudoCount | 0.000 | 0.000 | 0.001 | |
| clusterGraph | 0.570 | 0.013 | 0.583 | |
| clusterKmeans | 0.001 | 0.000 | 0.002 | |
| combineFactors | 0.002 | 0.000 | 0.003 | |
| computeClrm1Factors | 0.012 | 0.001 | 0.015 | |
| correctMnn | 0.289 | 0.002 | 0.292 | |
| crispr_quality_control | 0.012 | 0.001 | 0.013 | |
| fitVarianceTrend | 0.008 | 0.001 | 0.009 | |
| modelGeneVariances | 0.032 | 0.002 | 0.034 | |
| normalizeCounts | 0.089 | 0.002 | 0.092 | |
| rna_quality_control | 0.015 | 0.002 | 0.016 | |
| runAllNeighborSteps | 0.089 | 0.006 | 4.403 | |
| runPca | 0.094 | 0.005 | 0.103 | |
| runTsne | 0.161 | 0.001 | 0.164 | |
| runUmap | 0.169 | 0.000 | 0.170 | |
| sanitizeSizeFactors | 0.001 | 0.000 | 0.000 | |
| scaleByNeighbors | 0.082 | 0.001 | 0.082 | |
| scoreGeneSet | 0.036 | 0.001 | 0.037 | |
| scoreMarkers | 0.050 | 0.002 | 0.053 | |
| subsampleByNeighbors | 1.164 | 0.009 | 1.176 | |
| summarizeEffects | 0.051 | 0.002 | 0.053 | |