Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-25 11:42 -0400 (Thu, 25 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
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 1070/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.18.0 (landing page) Francesco Gazzo
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the ISAnalytics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ISAnalytics.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: ISAnalytics |
Version: 1.18.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ISAnalytics_1.18.0.tar.gz |
StartedAt: 2025-09-23 11:07:45 -0000 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 11:20:38 -0000 (Tue, 23 Sep 2025) |
EllapsedTime: 773.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ISAnalytics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ISAnalytics_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ISAnalytics/DESCRIPTION’ ... OK * this is package ‘ISAnalytics’ version ‘1.18.0’ * 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 ‘ISAnalytics’ 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 ... NOTE checkRd: (-1) refGenes_hg19.Rd:21: Lost braces; missing escapes or markup? 21 | \item Download from {http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/} | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed integration_alluvial_plot 4.239 0.180 14.519 sharing_venn 3.718 0.316 47.994 import_parallel_Vispa2Matrices 2.658 0.238 22.099 CIS_grubbs_overtime 1.969 0.153 8.692 top_cis_overtime_heatmap 1.956 0.127 12.202 sharing_heatmap 1.855 0.170 15.025 import_Vispa2_stats 1.628 0.182 10.285 iss_source 1.192 0.076 10.829 compute_near_integrations 1.085 0.099 11.921 HSC_population_plot 1.125 0.057 7.300 is_sharing 1.065 0.044 12.108 realign_after_collisions 0.973 0.072 9.524 remove_collisions 0.930 0.089 10.263 HSC_population_size_estimate 0.770 0.071 6.976 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck/00check.log’ for details.
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘ISAnalytics’ ... ** this is package ‘ISAnalytics’ version ‘1.18.0’ ** using staged installation ** R ** data ** 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 (ISAnalytics)
ISAnalytics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 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(ISAnalytics) > > test_check("ISAnalytics") Loading required namespace: plotly Loading required namespace: rmarkdown Report correctly saved i Report saved to: /home/biocbuild/tmp/Rtmp9tL2Rf/file2f87643944be4c/2025-09-23_collision_removal_report.html Report correctly saved i Report saved to: /home/biocbuild/tmp/Rtmp9tL2Rf/file2f87645629662a/2025-09-23_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 134.710 6.549 468.546
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 1.397 | 0.068 | 1.472 | |
CIS_grubbs_overtime | 1.969 | 0.153 | 8.692 | |
CIS_volcano_plot | 1.769 | 0.052 | 1.825 | |
HSC_population_plot | 1.125 | 0.057 | 7.300 | |
HSC_population_size_estimate | 0.770 | 0.071 | 6.976 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.153 | 0.004 | 0.158 | |
aggregate_values_by_key | 0.097 | 0.000 | 0.098 | |
annotation_issues | 0.04 | 0.00 | 0.04 | |
as_sparse_matrix | 0.060 | 0.028 | 0.088 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0.039 | 0.012 | 0.052 | |
blood_lineages_default | 0.030 | 0.004 | 0.034 | |
circos_genomic_density | 0.000 | 0.000 | 0.001 | |
clinical_relevant_suspicious_genes | 0.015 | 0.004 | 0.019 | |
comparison_matrix | 0.044 | 0.000 | 0.044 | |
compute_abundance | 0.049 | 0.000 | 0.049 | |
compute_near_integrations | 1.085 | 0.099 | 11.921 | |
cumulative_count_union | 0 | 0 | 0 | |
cumulative_is | 0.245 | 0.016 | 0.262 | |
date_formats | 0 | 0 | 0 | |
default_af_transform | 0 | 0 | 0 | |
default_iss_file_prefixes | 0 | 0 | 0 | |
default_meta_agg | 0.025 | 0.000 | 0.025 | |
default_rec_agg_lambdas | 0.001 | 0.000 | 0.001 | |
default_report_path | 0.006 | 0.004 | 0.010 | |
default_stats | 1.364 | 0.088 | 1.466 | |
enable_progress_bars | 0.017 | 0.004 | 0.020 | |
export_ISA_settings | 0.101 | 0.000 | 0.101 | |
fisher_scatterplot | 1.853 | 0.024 | 1.881 | |
gene_frequency_fisher | 1.275 | 0.044 | 1.322 | |
generate_Vispa2_launch_AF | 0.273 | 0.032 | 0.319 | |
generate_blank_association_file | 0.02 | 0.00 | 0.02 | |
generate_default_folder_structure | 0.615 | 0.028 | 1.101 | |
import_ISA_settings | 0.091 | 0.000 | 0.092 | |
import_Vispa2_stats | 1.628 | 0.182 | 10.285 | |
import_association_file | 0.894 | 0.145 | 1.232 | |
import_parallel_Vispa2Matrices | 2.658 | 0.238 | 22.099 | |
import_single_Vispa2Matrix | 1.191 | 0.030 | 1.575 | |
inspect_tags | 0.019 | 0.000 | 0.019 | |
integration_alluvial_plot | 4.239 | 0.180 | 14.519 | |
is_sharing | 1.065 | 0.044 | 12.108 | |
iss_source | 1.192 | 0.076 | 10.829 | |
known_clinical_oncogenes | 0.018 | 0.000 | 0.018 | |
mandatory_IS_vars | 0.134 | 0.032 | 0.167 | |
matching_options | 0.000 | 0.000 | 0.001 | |
outlier_filter | 0.199 | 0.016 | 0.215 | |
outliers_by_pool_fragments | 0.216 | 0.028 | 0.245 | |
pcr_id_column | 0.028 | 0.000 | 0.028 | |
purity_filter | 0.502 | 0.016 | 0.520 | |
quantification_types | 0.001 | 0.000 | 0.000 | |
realign_after_collisions | 0.973 | 0.072 | 9.524 | |
reduced_AF_columns | 0.059 | 0.000 | 0.059 | |
refGene_table_cols | 0 | 0 | 0 | |
remove_collisions | 0.930 | 0.089 | 10.263 | |
reset_mandatory_IS_vars | 0.008 | 0.000 | 0.007 | |
sample_statistics | 0.437 | 0.023 | 0.462 | |
separate_quant_matrices | 0.015 | 0.004 | 0.019 | |
set_mandatory_IS_vars | 0.146 | 0.016 | 0.162 | |
set_matrix_file_suffixes | 0.026 | 0.000 | 0.026 | |
sharing_heatmap | 1.855 | 0.170 | 15.025 | |
sharing_venn | 3.718 | 0.316 | 47.994 | |
threshold_filter | 0 | 0 | 0 | |
top_abund_tableGrob | 0.983 | 0.006 | 0.995 | |
top_cis_overtime_heatmap | 1.956 | 0.127 | 12.202 | |
top_integrations | 0.043 | 0.000 | 0.044 | |
top_targeted_genes | 0.699 | 0.027 | 0.727 | |
transform_columns | 0.047 | 0.000 | 0.047 | |