Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:41 -0500 (Mon, 23 Dec 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" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1883/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scrapper 1.1.8 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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: 1.1.8 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scrapper |
StartedAt: 2024-12-22 19:05:30 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 19:07:42 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 132.1 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scrapper ### ############################################################################## ############################################################################## * checking for file ‘scrapper/DESCRIPTION’ ... OK * preparing ‘scrapper’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * 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 In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/scran_pca/scran_pca.hpp:5, from run_pca.cpp:10: /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/scran_pca/blocked_pca.hpp: In function ‘void scran_pca::internal::project_matrix_realized_sparse(const IrlbaSparseMatrix_&, EigenMatrix_&, const EigenMatrix_&, int)’: /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/scran_pca/blocked_pca.hpp:514:16: error: ‘parallelize’ is not a member of ‘irlba’ 514 | irlba::parallelize(nthreads, [&](size_t t) -> void { | ^~~~~~~~~~~ /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/scran_pca/blocked_pca.hpp:514:16: note: suggested alternatives: In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include/Rtatami.h:6, from run_pca.cpp:9: /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_r/parallelize.hpp:61:6: note: ‘tatami_r::parallelize’ 61 | void parallelize(Function_ fun, Index_ njobs, int nthreads) { | ^~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami/dense/convert_to_dense.hpp:8, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami/tatami.hpp:5, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_r/UnknownMatrix.hpp:5, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_r/tatami_r.hpp:4, from /home/biocbuild/bbs-3.21-bioc/R/site-library/beachmat/include/Rtatami.h:8: /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami/dense/../utils/parallelize.hpp:42:6: note: ‘tatami::parallelize’ 42 | void parallelize(Function_ fun, Index_ tasks, int threads) { | ^~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/subpar/subpar.hpp:5, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_stats/counts.hpp:5, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:4, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/scran_pca/simple_pca.hpp:5, from /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/scran_pca/scran_pca.hpp:4: /home/biocbuild/bbs-3.21-bioc/R/site-library/assorthead/include/subpar/range.hpp:232:6: note: ‘subpar::parallelize’ 232 | void parallelize(int num_workers, Task_ num_tasks, Run_ run_task_range) { | ^~~~~~~~~~~ make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:202: run_pca.o] Error 1 ERROR: compilation failed for package ‘scrapper’ * removing ‘/tmp/RtmpOLwxcc/Rinst15a5cb2a77d545/scrapper’ ----------------------------------- ERROR: package installation failed