| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 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" | 4373 |
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scrapper |
| StartedAt: 2024-12-23 17:34:01 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 17:34:32 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 31.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scrapper
###
##############################################################################
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* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c adt_quality_control.cpp -o adt_quality_control.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c aggregate_across_cells.cpp -o aggregate_across_cells.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c aggregate_across_genes.cpp -o aggregate_across_genes.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c build_snn_graph.cpp -o build_snn_graph.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c center_size_factors.cpp -o center_size_factors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c choose_pseudo_count.cpp -o choose_pseudo_count.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cluster_graph.cpp -o cluster_graph.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cluster_kmeans.cpp -o cluster_kmeans.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c combine_factors.cpp -o combine_factors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c correct_mnn.cpp -o correct_mnn.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c crispr_quality_control.cpp -o crispr_quality_control.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c fit_variance_trend.cpp -o fit_variance_trend.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c model_gene_variances.cpp -o model_gene_variances.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c normalize_counts.cpp -o normalize_counts.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rna_quality_control.cpp -o rna_quality_control.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/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-arm64/Resources/library/assorthead/include/scran_pca/scran_pca.hpp:5:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:514:16: error: no member named 'parallelize' in namespace 'irlba'
irlba::parallelize(nthreads, [&](size_t t) -> void {
~~~~~~~^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:519:32: error: reference to local variable 'g' declared in enclosing lambda expression
for (size_t g = 0; g < ngenes; ++g) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:519:25: note: 'g' declared here
for (size_t g = 0; g < ngenes; ++g) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:519:46: error: reference to local variable 'g' declared in enclosing lambda expression
for (size_t g = 0; g < ngenes; ++g) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:519:25: note: 'g' declared here
for (size_t g = 0; g < ngenes; ++g) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:520:17: error: reference to local variable 'multipliers' declared in enclosing lambda expression
multipliers.noalias() = scaled_rotation.row(g);
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:517:29: note: 'multipliers' declared here
Eigen::VectorXd multipliers(rank);
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:520:61: error: reference to local variable 'g' declared in enclosing lambda expression
multipliers.noalias() = scaled_rotation.row(g);
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:519:25: note: 'g' declared here
for (size_t g = 0; g < ngenes; ++g) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:522:51: error: reference to local variable 's' declared in enclosing lambda expression
for (size_t s = start; s < end; ++s) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:522:29: note: 's' declared here
for (size_t s = start; s < end; ++s) {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:523:62: error: reference to local variable 'multipliers' declared in enclosing lambda expression
components.col(i[s]).noalias() += x[s] * multipliers;
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/blocked_pca.hpp:517:29: note: 'multipliers' declared here
Eigen::VectorXd multipliers(rank);
^
In file included from run_pca.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/scran_pca.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/assorthead/include/scran_pca/simple_pca.hpp:7:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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 and 7 errors generated.
make: *** [run_pca.o] Error 1
ERROR: compilation failed for package ‘scrapper’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp4tNVxq/Rinst486c30b8bd22/scrapper’
-----------------------------------
ERROR: package installation failed