Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:09 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1062/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.19.3 (landing page) Francesco Gazzo
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | 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: 1.19.3 |
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_1.19.3.tar.gz |
StartedAt: 2025-08-29 08:20:59 -0000 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 08:31:24 -0000 (Fri, 29 Aug 2025) |
EllapsedTime: 624.6 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_1.19.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ISAnalytics.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ISAnalytics/DESCRIPTION’ ... OK * this is package ‘ISAnalytics’ version ‘1.19.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... INFO installed size is 8.3Mb sub-directories of 1Mb or more: data 5.8Mb * 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 sharing_venn 5.025 0.239 44.234 integration_alluvial_plot 4.642 0.219 10.212 import_parallel_Vispa2Matrices 3.088 0.330 19.080 sharing_heatmap 2.243 0.145 13.089 import_Vispa2_stats 1.985 0.220 9.197 CIS_grubbs_overtime 1.997 0.147 8.780 is_sharing 1.543 0.554 11.736 top_cis_overtime_heatmap 1.962 0.126 10.082 HSC_population_plot 1.519 0.207 5.505 iss_source 1.452 0.151 9.801 remove_collisions 1.319 0.080 8.238 realign_after_collisions 1.272 0.083 8.269 HSC_population_size_estimate 1.156 0.134 7.302 compute_near_integrations 0.971 0.053 7.287 * 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-3.22-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-4.5.0/site-library’ * installing *source* package ‘ISAnalytics’ ... ** this is package ‘ISAnalytics’ version ‘1.19.3’ ** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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/Rtmp6s2LnN/file3dbf0a75bf3a73/2025-08-29_collision_removal_report.html Report correctly saved i Report saved to: /home/biocbuild/tmp/Rtmp6s2LnN/file3dbf0a1db7b1b0/2025-08-29_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 132.009 8.370 348.753
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 1.329 | 0.056 | 1.389 | |
CIS_grubbs_overtime | 1.997 | 0.147 | 8.780 | |
CIS_volcano_plot | 1.784 | 0.052 | 1.839 | |
HSC_population_plot | 1.519 | 0.207 | 5.505 | |
HSC_population_size_estimate | 1.156 | 0.134 | 7.302 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.149 | 0.000 | 0.149 | |
aggregate_values_by_key | 0.101 | 0.000 | 0.102 | |
annotation_issues | 0.038 | 0.000 | 0.039 | |
as_sparse_matrix | 0.071 | 0.000 | 0.071 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0.031 | 0.000 | 0.031 | |
blood_lineages_default | 0.031 | 0.000 | 0.031 | |
circos_genomic_density | 0 | 0 | 0 | |
clinical_relevant_suspicious_genes | 0.017 | 0.000 | 0.017 | |
comparison_matrix | 0.04 | 0.00 | 0.04 | |
compute_abundance | 0.050 | 0.004 | 0.055 | |
compute_near_integrations | 0.971 | 0.053 | 7.287 | |
cumulative_count_union | 0 | 0 | 0 | |
cumulative_is | 0.227 | 0.000 | 0.230 | |
date_formats | 0 | 0 | 0 | |
default_af_transform | 0.000 | 0.000 | 0.001 | |
default_iss_file_prefixes | 0 | 0 | 0 | |
default_meta_agg | 0.024 | 0.000 | 0.024 | |
default_rec_agg_lambdas | 0.000 | 0.000 | 0.001 | |
default_report_path | 0.01 | 0.00 | 0.01 | |
default_stats | 1.394 | 0.055 | 1.465 | |
enable_progress_bars | 0.02 | 0.00 | 0.02 | |
export_ISA_settings | 0.101 | 0.000 | 0.102 | |
fisher_scatterplot | 1.425 | 0.088 | 1.519 | |
gene_frequency_fisher | 1.268 | 0.036 | 1.309 | |
generate_Vispa2_launch_AF | 0.248 | 0.014 | 0.262 | |
generate_blank_association_file | 0.017 | 0.000 | 0.017 | |
generate_default_folder_structure | 0.514 | 0.095 | 0.609 | |
import_ISA_settings | 0.089 | 0.004 | 0.093 | |
import_Vispa2_stats | 1.985 | 0.220 | 9.197 | |
import_association_file | 0.807 | 0.165 | 0.977 | |
import_parallel_Vispa2Matrices | 3.088 | 0.330 | 19.080 | |
import_single_Vispa2Matrix | 1.060 | 0.189 | 1.254 | |
inspect_tags | 0.020 | 0.000 | 0.021 | |
integration_alluvial_plot | 4.642 | 0.219 | 10.212 | |
is_sharing | 1.543 | 0.554 | 11.736 | |
iss_source | 1.452 | 0.151 | 9.801 | |
known_clinical_oncogenes | 0.016 | 0.000 | 0.016 | |
mandatory_IS_vars | 0.130 | 0.004 | 0.134 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.215 | 0.020 | 0.236 | |
outliers_by_pool_fragments | 0.213 | 0.000 | 0.213 | |
pcr_id_column | 0.027 | 0.004 | 0.032 | |
purity_filter | 0.476 | 0.040 | 0.518 | |
quantification_types | 0 | 0 | 0 | |
realign_after_collisions | 1.272 | 0.083 | 8.269 | |
reduced_AF_columns | 0.065 | 0.000 | 0.065 | |
refGene_table_cols | 0.001 | 0.000 | 0.000 | |
remove_collisions | 1.319 | 0.080 | 8.238 | |
reset_mandatory_IS_vars | 0.008 | 0.000 | 0.008 | |
sample_statistics | 0.489 | 0.008 | 0.499 | |
separate_quant_matrices | 0.022 | 0.000 | 0.022 | |
set_mandatory_IS_vars | 0.149 | 0.036 | 0.185 | |
set_matrix_file_suffixes | 0.020 | 0.007 | 0.027 | |
sharing_heatmap | 2.243 | 0.145 | 13.089 | |
sharing_venn | 5.025 | 0.239 | 44.234 | |
threshold_filter | 0.000 | 0.000 | 0.001 | |
top_abund_tableGrob | 0.926 | 0.056 | 0.985 | |
top_cis_overtime_heatmap | 1.962 | 0.126 | 10.082 | |
top_integrations | 0.041 | 0.000 | 0.041 | |
top_targeted_genes | 0.686 | 0.007 | 0.695 | |
transform_columns | 0.029 | 0.000 | 0.029 | |