Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-09-22 11:41 -0400 (Mon, 22 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: 2025-09-19 11:06:22 -0000 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 11:18:33 -0000 (Fri, 19 Sep 2025) |
EllapsedTime: 731.9 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 4.416 0.307 14.148 sharing_venn 3.789 0.221 45.148 import_parallel_Vispa2Matrices 2.615 0.368 21.803 CIS_grubbs_overtime 2.051 0.267 8.884 import_Vispa2_stats 1.774 0.172 10.502 top_cis_overtime_heatmap 1.868 0.074 11.526 sharing_heatmap 1.789 0.115 13.938 iss_source 1.198 0.102 10.934 HSC_population_plot 1.158 0.081 7.252 compute_near_integrations 1.122 0.074 11.791 is_sharing 1.069 0.075 11.767 realign_after_collisions 0.973 0.077 9.385 remove_collisions 0.964 0.069 9.320 HSC_population_size_estimate 0.828 0.016 7.000 * 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/RtmpqRT6Qa/file29510a5caee936/2025-09-19_collision_removal_report.html Report correctly saved i Report saved to: /home/biocbuild/tmp/RtmpqRT6Qa/file29510a7601cc5a/2025-09-19_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 134.096 9.231 432.863
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 1.395 | 0.048 | 1.446 | |
CIS_grubbs_overtime | 2.051 | 0.267 | 8.884 | |
CIS_volcano_plot | 1.880 | 0.140 | 2.023 | |
HSC_population_plot | 1.158 | 0.081 | 7.252 | |
HSC_population_size_estimate | 0.828 | 0.016 | 7.000 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.174 | 0.023 | 0.199 | |
aggregate_values_by_key | 0.105 | 0.000 | 0.106 | |
annotation_issues | 0.041 | 0.000 | 0.041 | |
as_sparse_matrix | 0.077 | 0.004 | 0.081 | |
available_outlier_tests | 0.001 | 0.000 | 0.000 | |
available_tags | 0.043 | 0.000 | 0.043 | |
blood_lineages_default | 0.034 | 0.000 | 0.034 | |
circos_genomic_density | 0 | 0 | 0 | |
clinical_relevant_suspicious_genes | 0.020 | 0.000 | 0.021 | |
comparison_matrix | 0.047 | 0.000 | 0.048 | |
compute_abundance | 0.055 | 0.000 | 0.055 | |
compute_near_integrations | 1.122 | 0.074 | 11.791 | |
cumulative_count_union | 0 | 0 | 0 | |
cumulative_is | 0.244 | 0.012 | 0.256 | |
date_formats | 0.001 | 0.000 | 0.000 | |
default_af_transform | 0.000 | 0.000 | 0.001 | |
default_iss_file_prefixes | 0.000 | 0.000 | 0.001 | |
default_meta_agg | 0.024 | 0.000 | 0.025 | |
default_rec_agg_lambdas | 0.000 | 0.000 | 0.001 | |
default_report_path | 0.009 | 0.000 | 0.010 | |
default_stats | 1.404 | 0.116 | 1.523 | |
enable_progress_bars | 0.019 | 0.002 | 0.022 | |
export_ISA_settings | 0.107 | 0.000 | 0.107 | |
fisher_scatterplot | 1.881 | 0.036 | 1.920 | |
gene_frequency_fisher | 1.305 | 0.016 | 1.324 | |
generate_Vispa2_launch_AF | 0.265 | 0.020 | 0.284 | |
generate_blank_association_file | 0.019 | 0.000 | 0.020 | |
generate_default_folder_structure | 0.512 | 0.114 | 0.627 | |
import_ISA_settings | 0.105 | 0.000 | 0.106 | |
import_Vispa2_stats | 1.774 | 0.172 | 10.502 | |
import_association_file | 0.861 | 0.136 | 0.998 | |
import_parallel_Vispa2Matrices | 2.615 | 0.368 | 21.803 | |
import_single_Vispa2Matrix | 1.236 | 0.256 | 1.495 | |
inspect_tags | 0.019 | 0.000 | 0.020 | |
integration_alluvial_plot | 4.416 | 0.307 | 14.148 | |
is_sharing | 1.069 | 0.075 | 11.767 | |
iss_source | 1.198 | 0.102 | 10.934 | |
known_clinical_oncogenes | 0.015 | 0.000 | 0.016 | |
mandatory_IS_vars | 0.140 | 0.012 | 0.153 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.193 | 0.016 | 0.210 | |
outliers_by_pool_fragments | 0.225 | 0.004 | 0.230 | |
pcr_id_column | 0.023 | 0.004 | 0.027 | |
purity_filter | 0.470 | 0.028 | 0.499 | |
quantification_types | 0 | 0 | 0 | |
realign_after_collisions | 0.973 | 0.077 | 9.385 | |
reduced_AF_columns | 0.062 | 0.004 | 0.066 | |
refGene_table_cols | 0.001 | 0.000 | 0.001 | |
remove_collisions | 0.964 | 0.069 | 9.320 | |
reset_mandatory_IS_vars | 0.007 | 0.000 | 0.007 | |
sample_statistics | 0.424 | 0.043 | 0.470 | |
separate_quant_matrices | 0.020 | 0.001 | 0.020 | |
set_mandatory_IS_vars | 0.144 | 0.000 | 0.144 | |
set_matrix_file_suffixes | 0.027 | 0.000 | 0.026 | |
sharing_heatmap | 1.789 | 0.115 | 13.938 | |
sharing_venn | 3.789 | 0.221 | 45.148 | |
threshold_filter | 0 | 0 | 0 | |
top_abund_tableGrob | 1.062 | 0.004 | 1.068 | |
top_cis_overtime_heatmap | 1.868 | 0.074 | 11.526 | |
top_integrations | 0.037 | 0.000 | 0.038 | |
top_targeted_genes | 0.632 | 0.000 | 0.635 | |
transform_columns | 0.041 | 0.000 | 0.041 | |