Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-14 11:46 -0400 (Thu, 14 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | 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. |
Package: ISAnalytics |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ISAnalytics_1.18.0.tar.gz |
StartedAt: 2025-08-12 23:44:55 -0400 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 23:54:54 -0400 (Tue, 12 Aug 2025) |
EllapsedTime: 599.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ISAnalytics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ISAnalytics_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * 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 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 3.707 0.108 11.239 import_parallel_Vispa2Matrices 2.985 0.189 17.745 sharing_venn 2.339 0.132 37.323 top_cis_overtime_heatmap 2.043 0.092 10.674 import_Vispa2_stats 1.894 0.187 8.572 CIS_grubbs_overtime 1.781 0.210 8.001 sharing_heatmap 1.530 0.066 10.869 is_sharing 1.414 0.070 9.820 iss_source 1.427 0.037 9.063 realign_after_collisions 1.345 0.053 7.929 remove_collisions 1.339 0.038 7.959 HSC_population_plot 1.224 0.036 7.113 compute_near_integrations 1.021 0.044 10.744 HSC_population_size_estimate 0.997 0.031 6.785 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck/00check.log’ for details.
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 2025-08-12 23:50:12.338 R[20575:293763946] XType: Using static font registry. Report correctly saved i Report saved to: /tmp/RtmpkrFLiD/file505f2e46195d/2025-08-12_collision_removal_report.html Report correctly saved i Report saved to: /tmp/RtmpkrFLiD/file505f126a19f/2025-08-12_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 102.686 5.554 342.810
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 1.117 | 0.057 | 1.177 | |
CIS_grubbs_overtime | 1.781 | 0.210 | 8.001 | |
CIS_volcano_plot | 1.152 | 0.029 | 1.194 | |
HSC_population_plot | 1.224 | 0.036 | 7.113 | |
HSC_population_size_estimate | 0.997 | 0.031 | 6.785 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.106 | 0.003 | 0.110 | |
aggregate_values_by_key | 0.078 | 0.008 | 0.086 | |
annotation_issues | 0.031 | 0.003 | 0.034 | |
as_sparse_matrix | 0.054 | 0.003 | 0.056 | |
available_outlier_tests | 0.000 | 0.000 | 0.001 | |
available_tags | 0.02 | 0.00 | 0.02 | |
blood_lineages_default | 0.02 | 0.00 | 0.02 | |
circos_genomic_density | 0 | 0 | 0 | |
clinical_relevant_suspicious_genes | 0.012 | 0.000 | 0.012 | |
comparison_matrix | 0.027 | 0.000 | 0.028 | |
compute_abundance | 0.047 | 0.003 | 0.050 | |
compute_near_integrations | 1.021 | 0.044 | 10.744 | |
cumulative_count_union | 0 | 0 | 0 | |
cumulative_is | 0.175 | 0.005 | 0.181 | |
date_formats | 0.000 | 0.000 | 0.001 | |
default_af_transform | 0.001 | 0.001 | 0.001 | |
default_iss_file_prefixes | 0.001 | 0.000 | 0.000 | |
default_meta_agg | 0.016 | 0.001 | 0.017 | |
default_rec_agg_lambdas | 0.001 | 0.000 | 0.000 | |
default_report_path | 0.008 | 0.001 | 0.009 | |
default_stats | 1.173 | 0.072 | 1.246 | |
enable_progress_bars | 0.019 | 0.003 | 0.023 | |
export_ISA_settings | 0.071 | 0.005 | 0.076 | |
fisher_scatterplot | 1.117 | 0.034 | 1.158 | |
gene_frequency_fisher | 0.935 | 0.021 | 0.956 | |
generate_Vispa2_launch_AF | 0.219 | 0.027 | 0.253 | |
generate_blank_association_file | 0.014 | 0.001 | 0.015 | |
generate_default_folder_structure | 0.400 | 0.113 | 0.469 | |
import_ISA_settings | 0.062 | 0.002 | 0.064 | |
import_Vispa2_stats | 1.894 | 0.187 | 8.572 | |
import_association_file | 0.640 | 0.146 | 0.710 | |
import_parallel_Vispa2Matrices | 2.985 | 0.189 | 17.745 | |
import_single_Vispa2Matrix | 1.002 | 0.149 | 1.082 | |
inspect_tags | 0.014 | 0.000 | 0.015 | |
integration_alluvial_plot | 3.707 | 0.108 | 11.239 | |
is_sharing | 1.414 | 0.070 | 9.820 | |
iss_source | 1.427 | 0.037 | 9.063 | |
known_clinical_oncogenes | 0.013 | 0.001 | 0.013 | |
mandatory_IS_vars | 0.094 | 0.009 | 0.103 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.160 | 0.018 | 0.178 | |
outliers_by_pool_fragments | 0.176 | 0.013 | 0.189 | |
pcr_id_column | 0.02 | 0.00 | 0.02 | |
purity_filter | 0.328 | 0.007 | 0.335 | |
quantification_types | 0 | 0 | 0 | |
realign_after_collisions | 1.345 | 0.053 | 7.929 | |
reduced_AF_columns | 0.041 | 0.000 | 0.041 | |
refGene_table_cols | 0.001 | 0.000 | 0.001 | |
remove_collisions | 1.339 | 0.038 | 7.959 | |
reset_mandatory_IS_vars | 0.005 | 0.000 | 0.005 | |
sample_statistics | 0.315 | 0.057 | 0.377 | |
separate_quant_matrices | 0.019 | 0.003 | 0.024 | |
set_mandatory_IS_vars | 0.099 | 0.009 | 0.110 | |
set_matrix_file_suffixes | 0.022 | 0.002 | 0.023 | |
sharing_heatmap | 1.530 | 0.066 | 10.869 | |
sharing_venn | 2.339 | 0.132 | 37.323 | |
threshold_filter | 0.000 | 0.001 | 0.000 | |
top_abund_tableGrob | 0.651 | 0.013 | 0.664 | |
top_cis_overtime_heatmap | 2.043 | 0.092 | 10.674 | |
top_integrations | 0.032 | 0.003 | 0.036 | |
top_targeted_genes | 0.428 | 0.015 | 0.447 | |
transform_columns | 0.020 | 0.000 | 0.021 | |