Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-08 12:08 -0400 (Fri, 08 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 1059/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.19.3 (landing page) Francesco Gazzo
| nebbiolo2 | Linux (Ubuntu 24.04.2 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 13.7.1 Ventura / arm64 | OK | 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: 1.19.3 |
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_1.19.3.tar.gz |
StartedAt: 2025-08-07 21:48:01 -0400 (Thu, 07 Aug 2025) |
EndedAt: 2025-08-07 21:59:10 -0400 (Thu, 07 Aug 2025) |
EllapsedTime: 669.9 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_1.19.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ISAnalytics.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 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 3.816 0.092 11.537 import_parallel_Vispa2Matrices 2.726 0.159 18.746 sharing_venn 2.475 0.120 41.955 CIS_grubbs_overtime 1.924 0.247 9.072 import_Vispa2_stats 1.785 0.157 8.927 top_cis_overtime_heatmap 1.780 0.068 10.907 sharing_heatmap 1.797 0.049 12.356 iss_source 1.350 0.032 10.990 is_sharing 1.299 0.043 12.094 realign_after_collisions 1.212 0.037 8.297 HSC_population_plot 1.183 0.032 7.425 remove_collisions 1.184 0.024 8.104 compute_near_integrations 0.962 0.038 12.046 HSC_population_size_estimate 0.860 0.026 7.301 * 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-3.22-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-x86_64/Resources/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 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 2025-08-07 21:53:56.616 R[22759:407284130] XType: com.apple.fonts is not accessible. 2025-08-07 21:53:56.616 R[22759:407284130] XType: XTFontStaticRegistry is enabled. Report correctly saved i Report saved to: /tmp/RtmpMu6RNF/file58e765c645ff/2025-08-07_collision_removal_report.html Report correctly saved i Report saved to: /tmp/RtmpMu6RNF/file58e74d2261f5/2025-08-07_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 114.243 5.661 382.060
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 1.060 | 0.053 | 1.116 | |
CIS_grubbs_overtime | 1.924 | 0.247 | 9.072 | |
CIS_volcano_plot | 1.361 | 0.026 | 1.392 | |
HSC_population_plot | 1.183 | 0.032 | 7.425 | |
HSC_population_size_estimate | 0.860 | 0.026 | 7.301 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.120 | 0.002 | 0.123 | |
aggregate_values_by_key | 0.096 | 0.003 | 0.101 | |
annotation_issues | 0.036 | 0.001 | 0.038 | |
as_sparse_matrix | 0.060 | 0.002 | 0.062 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0.024 | 0.000 | 0.024 | |
blood_lineages_default | 0.030 | 0.001 | 0.030 | |
circos_genomic_density | 0 | 0 | 0 | |
clinical_relevant_suspicious_genes | 0.015 | 0.000 | 0.016 | |
comparison_matrix | 0.035 | 0.001 | 0.036 | |
compute_abundance | 0.055 | 0.002 | 0.057 | |
compute_near_integrations | 0.962 | 0.038 | 12.046 | |
cumulative_count_union | 0 | 0 | 0 | |
cumulative_is | 0.192 | 0.004 | 0.197 | |
date_formats | 0 | 0 | 0 | |
default_af_transform | 0.001 | 0.000 | 0.001 | |
default_iss_file_prefixes | 0.000 | 0.001 | 0.000 | |
default_meta_agg | 0.019 | 0.000 | 0.020 | |
default_rec_agg_lambdas | 0.000 | 0.000 | 0.001 | |
default_report_path | 0.007 | 0.002 | 0.009 | |
default_stats | 1.156 | 0.046 | 1.212 | |
enable_progress_bars | 0.015 | 0.003 | 0.018 | |
export_ISA_settings | 0.080 | 0.006 | 0.086 | |
fisher_scatterplot | 1.155 | 0.024 | 1.186 | |
gene_frequency_fisher | 1.010 | 0.016 | 1.038 | |
generate_Vispa2_launch_AF | 0.230 | 0.019 | 0.260 | |
generate_blank_association_file | 0.012 | 0.000 | 0.013 | |
generate_default_folder_structure | 0.441 | 0.080 | 0.471 | |
import_ISA_settings | 0.069 | 0.002 | 0.071 | |
import_Vispa2_stats | 1.785 | 0.157 | 8.927 | |
import_association_file | 0.696 | 0.106 | 0.740 | |
import_parallel_Vispa2Matrices | 2.726 | 0.159 | 18.746 | |
import_single_Vispa2Matrix | 0.987 | 0.127 | 1.069 | |
inspect_tags | 0.015 | 0.000 | 0.016 | |
integration_alluvial_plot | 3.816 | 0.092 | 11.537 | |
is_sharing | 1.299 | 0.043 | 12.094 | |
iss_source | 1.350 | 0.032 | 10.990 | |
known_clinical_oncogenes | 0.013 | 0.001 | 0.014 | |
mandatory_IS_vars | 0.112 | 0.004 | 0.117 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.194 | 0.012 | 0.208 | |
outliers_by_pool_fragments | 0.219 | 0.007 | 0.227 | |
pcr_id_column | 0.022 | 0.000 | 0.023 | |
purity_filter | 0.382 | 0.004 | 0.389 | |
quantification_types | 0 | 0 | 0 | |
realign_after_collisions | 1.212 | 0.037 | 8.297 | |
reduced_AF_columns | 0.049 | 0.001 | 0.049 | |
refGene_table_cols | 0.000 | 0.000 | 0.001 | |
remove_collisions | 1.184 | 0.024 | 8.104 | |
reset_mandatory_IS_vars | 0.006 | 0.000 | 0.007 | |
sample_statistics | 0.381 | 0.045 | 0.427 | |
separate_quant_matrices | 0.016 | 0.001 | 0.018 | |
set_mandatory_IS_vars | 0.106 | 0.003 | 0.110 | |
set_matrix_file_suffixes | 0.024 | 0.001 | 0.025 | |
sharing_heatmap | 1.797 | 0.049 | 12.356 | |
sharing_venn | 2.475 | 0.120 | 41.955 | |
threshold_filter | 0.001 | 0.001 | 0.000 | |
top_abund_tableGrob | 0.754 | 0.010 | 0.767 | |
top_cis_overtime_heatmap | 1.780 | 0.068 | 10.907 | |
top_integrations | 0.037 | 0.001 | 0.038 | |
top_targeted_genes | 0.533 | 0.007 | 0.542 | |
transform_columns | 0.024 | 0.001 | 0.024 | |