Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-19 11:45 -0400 (Mon, 19 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1899/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqArchR 1.9.0 (landing page) Sarvesh Nikumbh
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the seqArchR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqArchR.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: seqArchR |
Version: 1.9.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:seqArchR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqArchR_1.9.0.tar.gz |
StartedAt: 2024-08-19 09:32:30 -0000 (Mon, 19 Aug 2024) |
EndedAt: 2024-08-19 09:35:07 -0000 (Mon, 19 Aug 2024) |
EllapsedTime: 157.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: seqArchR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:seqArchR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings seqArchR_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/seqArchR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqArchR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqArchR’ version ‘1.9.0’ * 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 ‘seqArchR’ can be installed ... OK * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘seqArchR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: seqArchR > ### Title: seqArchR: A package for de novo discovery of different sequence > ### architectures > ### Aliases: seqArchR > > ### ** Examples > > > > # Here,we re-use the example input sequences and one-hot encoded matrix > # shipped with seqArchR. Please see examples in the corresponding man pages > # for generating a one-hot encoded input matrix from raw FASTA sequences > # in `prepare_data_from_FASTA` > # > inputSeqsMat <- readRDS(system.file("extdata", "tssSinuc.rds", + package = "seqArchR", mustWork = TRUE)) > > inputSeqsRaw <- readRDS(system.file("extdata", "tssSeqsRaw.rds", + package = "seqArchR", mustWork = TRUE)) > > # Set seqArchR configuration > seqArchRconfig <- seqArchR::set_config( + parallelize = TRUE, + n_cores = 2, + n_runs = 100, + k_min = 1, + k_max = 20, + mod_sel_type = "stability", + bound = 10^-8, + chunk_size = 100, + flags = list(debug = FALSE, time = TRUE, verbose = TRUE, + plot = FALSE) + ) > > # Run seqArchR > seqArchRresult <- seqArchR::seqArchR(config = seqArchRconfig, + seqs_ohe_mat = inputSeqsMat, + seqs_raw = inputSeqsRaw, + seqs_pos = seq(1,100,by=1), + total_itr = 2, + set_ocollation = c(TRUE, FALSE)) ── Setting up ────────────────────────────────────────────────────────────────── ℹ Parallelization: Yes ℹ Model selection by factor stability ℹ Bound: 1e-08 ── Iteration 1 of 2 [1 chunk] ────────────────────────────────────────────────── ── Outer chunk 1 of 1 [Size: 200] ── ── Inner chunk 1 of 2 [Size: 100] Error: BiocParallel errors 2 remote errors, element index: 1, 51 98 unevaluated and other errors first remote error: Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn' Run `reticulate::py_last_error()` for details. Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ▆ 1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:186:5 2. └─seqArchR:::process_innerChunk(...) 3. └─base::lapply(...) 4. └─seqArchR (local) FUN(X[[i]], ...) 5. └─seqArchR:::.handle_chunk_w_NMF2(...) 6. └─seqArchR:::.stability_model_select_pyNMF2(...) 7. └─seqArchR:::.perform_multiple_NMF_runs(...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...) 10. └─BiocParallel:::.bpinit(...) [ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ] Error: Test failures Execution halted * 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 ERRORs See ‘/home/biocbuild/bbs-3.20-bioc/meat/seqArchR.Rcheck/00check.log’ for details.
seqArchR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL seqArchR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘seqArchR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (seqArchR)
seqArchR.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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(seqArchR) > > test_check("seqArchR") [[1]] NULL [ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test_plot_arch_for_clusters.R:31:5', 'test_plot_ggseqlogo.R:75:3', 'test_plot_heatmap.R:61:3', 'test_seqs_image_representation.R:15:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_seqArchR_main.R:48:5'): seqArchR (stability) works when timeFlag is FALSE/checkpointing ── <bplist_error/bperror/error/condition> Error: BiocParallel errors 1 remote errors, element index: 1 49 unevaluated and other errors first remote error: Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn' Run `reticulate::py_last_error()` for details. Backtrace: ▆ 1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:48:5 2. └─seqArchR:::process_innerChunk(...) 3. └─base::lapply(...) 4. └─seqArchR (local) FUN(X[[i]], ...) 5. └─seqArchR:::.handle_chunk_w_NMF2(...) 6. └─seqArchR:::.stability_model_select_pyNMF2(...) 7. └─seqArchR:::.perform_multiple_NMF_runs(...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...) 10. └─BiocParallel:::.bpinit(...) ── Error ('test_seqArchR_main.R:149:5'): seqArchR (cv) works when timeFlag is FALSE ── <bplist_error/bperror/error/condition> Error: BiocParallel errors 2 remote errors, element index: 1, 26 48 unevaluated and other errors first remote error: Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn' Run `reticulate::py_last_error()` for details. Backtrace: ▆ 1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:149:5 2. └─seqArchR:::process_innerChunk(...) 3. └─base::lapply(...) 4. └─seqArchR (local) FUN(X[[i]], ...) 5. └─seqArchR:::.handle_chunk_w_NMF2(...) 6. └─seqArchR:::.cv_model_select_pyNMF2(...) 7. └─seqArchR:::performSearchForK(...) 8. ├─base::unlist(...) 9. ├─BiocParallel::bplapply(...) 10. └─BiocParallel::bplapply(...) 11. └─BiocParallel:::.bpinit(...) ── Error ('test_seqArchR_main.R:186:5'): seqArchR (stability) works when debug & timeFlag is FALSE ── <bplist_error/bperror/error/condition> Error: BiocParallel errors 1 remote errors, element index: 1 49 unevaluated and other errors first remote error: Error in py_run_file_impl(file, local, convert): ModuleNotFoundError: No module named 'sklearn' Run `reticulate::py_last_error()` for details. Backtrace: ▆ 1. └─seqArchR::seqArchR(...) at test_seqArchR_main.R:186:5 2. └─seqArchR:::process_innerChunk(...) 3. └─base::lapply(...) 4. └─seqArchR (local) FUN(X[[i]], ...) 5. └─seqArchR:::.handle_chunk_w_NMF2(...) 6. └─seqArchR:::.stability_model_select_pyNMF2(...) 7. └─seqArchR:::.perform_multiple_NMF_runs(...) 8. ├─BiocParallel::bplapply(...) 9. └─BiocParallel::bplapply(...) 10. └─BiocParallel:::.bpinit(...) [ FAIL 3 | WARN 0 | SKIP 4 | PASS 101 ] Error: Test failures Execution halted
seqArchR.Rcheck/seqArchR-Ex.timings
name | user | system | elapsed | |
collate_clusters | 0.001 | 0.000 | 0.001 | |
collate_seqArchR_result | 0.966 | 0.004 | 0.973 | |
get_clBasVec | 0.018 | 0.004 | 0.023 | |
get_one_hot_encoded_seqs | 0.411 | 0.020 | 0.433 | |
get_seqs_clust_list | 0.001 | 0.000 | 0.000 | |
make_PWMs | 0.057 | 0.000 | 0.056 | |
plot_arch_for_clusters | 4.717 | 0.048 | 4.778 | |
plot_ggseqlogo_of_seqs | 1.141 | 0.000 | 1.144 | |
prepare_data_from_FASTA | 0.502 | 0.008 | 0.511 | |