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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1070/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.18.0  (landing page)
Francesco Gazzo
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: RELEASE_3_21
git_last_commit: 6c72216
git_last_commit_date: 2025-04-15 12:07:52 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ISAnalytics on kjohnson1

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.

raw results


Summary

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: 2025-10-15 01:16:59 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 01:27:51 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 651.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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      3.645  0.121  11.715
import_parallel_Vispa2Matrices 2.851  0.176  19.311
sharing_venn                   2.608  0.155  37.429
CIS_grubbs_overtime            2.047  0.210   8.760
sharing_heatmap                2.175  0.066  13.950
import_Vispa2_stats            1.969  0.206   9.484
top_cis_overtime_heatmap       2.067  0.081  11.033
iss_source                     1.688  0.042  10.159
is_sharing                     1.572  0.042  10.928
HSC_population_plot            1.435  0.045   7.646
realign_after_collisions       1.433  0.037   8.467
remove_collisions              1.414  0.030   8.431
compute_near_integrations      1.063  0.040  11.694
HSC_population_size_estimate   1.017  0.031   7.064
* 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.


Installation output

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)

Tests output

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
2025-10-15 01:22:47.528 R[41061:457831065] XType: Using static font registry.
Report correctly saved
i Report saved to: /tmp/RtmpWBFV6x/filea06587cdc2f/2025-10-15_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpWBFV6x/filea06541e85219/2025-10-15_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
108.755   5.110 370.919 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs0.9520.0471.012
CIS_grubbs_overtime2.0470.2108.760
CIS_volcano_plot1.6350.0451.722
HSC_population_plot1.4350.0457.646
HSC_population_size_estimate1.0170.0317.064
NGSdataExplorer000
aggregate_metadata0.1080.0030.110
aggregate_values_by_key0.0730.0040.077
annotation_issues0.0350.0020.038
as_sparse_matrix0.0590.0020.064
available_outlier_tests000
available_tags0.0240.0010.025
blood_lineages_default0.0310.0000.032
circos_genomic_density0.0010.0000.000
clinical_relevant_suspicious_genes0.0120.0000.013
comparison_matrix0.0300.0000.032
compute_abundance0.0390.0030.042
compute_near_integrations 1.063 0.04011.694
cumulative_count_union0.0000.0010.000
cumulative_is0.1770.0060.186
date_formats000
default_af_transform0.0010.0010.001
default_iss_file_prefixes0.0010.0000.000
default_meta_agg0.0160.0000.017
default_rec_agg_lambdas000
default_report_path0.0070.0010.009
default_stats1.3650.0371.413
enable_progress_bars0.0180.0020.021
export_ISA_settings0.0740.0030.077
fisher_scatterplot1.0200.0911.123
gene_frequency_fisher0.7960.0230.831
generate_Vispa2_launch_AF0.2200.0300.251
generate_blank_association_file0.0160.0010.020
generate_default_folder_structure0.9140.1451.025
import_ISA_settings0.0770.0040.082
import_Vispa2_stats1.9690.2069.484
import_association_file0.4020.1150.464
import_parallel_Vispa2Matrices 2.851 0.17619.311
import_single_Vispa2Matrix1.0180.1601.103
inspect_tags0.0130.0000.013
integration_alluvial_plot 3.645 0.12111.715
is_sharing 1.572 0.04210.928
iss_source 1.688 0.04210.159
known_clinical_oncogenes0.0120.0010.014
mandatory_IS_vars0.0810.0070.089
matching_options0.0000.0000.001
outlier_filter0.1640.0120.177
outliers_by_pool_fragments0.1210.0030.128
pcr_id_column0.0130.0000.013
purity_filter0.2880.0050.295
quantification_types0.0000.0000.001
realign_after_collisions1.4330.0378.467
reduced_AF_columns0.0450.0000.045
refGene_table_cols000
remove_collisions1.4140.0308.431
reset_mandatory_IS_vars0.0050.0010.005
sample_statistics0.3130.0500.363
separate_quant_matrices0.0180.0020.020
set_mandatory_IS_vars0.0910.0050.097
set_matrix_file_suffixes0.0200.0010.021
sharing_heatmap 2.175 0.06613.950
sharing_venn 2.608 0.15537.429
threshold_filter0.0000.0010.000
top_abund_tableGrob0.6390.0100.650
top_cis_overtime_heatmap 2.067 0.08111.033
top_integrations0.0320.0010.033
top_targeted_genes0.4180.0070.428
transform_columns0.0200.0000.021