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This page was generated on 2025-08-18 11:45 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 1070/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.18.0  (landing page)
Francesco Gazzo
Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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: 2025-08-16 00:05:21 -0400 (Sat, 16 Aug 2025)
EndedAt: 2025-08-16 00:15:26 -0400 (Sat, 16 Aug 2025)
EllapsedTime: 604.4 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      3.618  0.098  10.742
import_parallel_Vispa2Matrices 2.922  0.183  17.969
sharing_venn                   2.565  0.155  37.287
CIS_grubbs_overtime            1.947  0.215   8.216
top_cis_overtime_heatmap       2.044  0.099  10.600
import_Vispa2_stats            1.836  0.170   8.498
sharing_heatmap                1.900  0.067  11.301
iss_source                     1.417  0.035  10.163
realign_after_collisions       1.363  0.044   7.867
remove_collisions              1.274  0.029   7.817
HSC_population_plot            1.191  0.032   6.800
is_sharing                     1.133  0.056   9.464
compute_near_integrations      1.051  0.046  10.976
HSC_population_size_estimate   0.937  0.031   6.563
* 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
2025-08-16 00:10:40.415 R[78258:303015571] XType: Using static font registry.
Report correctly saved
i Report saved to: /tmp/Rtmp1gtsg9/file131b21ac87863/2025-08-16_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/Rtmp1gtsg9/file131b21df3c4f7/2025-08-16_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
103.593   5.461 347.336 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.1300.0521.190
CIS_grubbs_overtime1.9470.2158.216
CIS_volcano_plot1.3350.0301.366
HSC_population_plot1.1910.0326.800
HSC_population_size_estimate0.9370.0316.563
NGSdataExplorer000
aggregate_metadata0.1090.0030.114
aggregate_values_by_key0.0830.0060.090
annotation_issues0.0310.0020.033
as_sparse_matrix0.0560.0040.061
available_outlier_tests000
available_tags0.020.000.02
blood_lineages_default0.0200.0010.022
circos_genomic_density000
clinical_relevant_suspicious_genes0.0140.0000.016
comparison_matrix0.0330.0020.036
compute_abundance0.0500.0030.055
compute_near_integrations 1.051 0.04610.976
cumulative_count_union000
cumulative_is0.1740.0050.179
date_formats000
default_af_transform0.0000.0000.001
default_iss_file_prefixes000
default_meta_agg0.0190.0000.020
default_rec_agg_lambdas0.0010.0000.000
default_report_path0.0100.0020.011
default_stats1.1580.0541.211
enable_progress_bars0.0180.0030.023
export_ISA_settings0.0720.0060.079
fisher_scatterplot1.1280.0391.167
gene_frequency_fisher0.9470.0190.967
generate_Vispa2_launch_AF0.2230.0240.254
generate_blank_association_file0.0140.0010.018
generate_default_folder_structure0.4030.1110.468
import_ISA_settings0.0640.0020.074
import_Vispa2_stats1.8360.1708.498
import_association_file0.6260.1490.694
import_parallel_Vispa2Matrices 2.922 0.18317.969
import_single_Vispa2Matrix1.0010.1541.079
inspect_tags0.0140.0000.015
integration_alluvial_plot 3.618 0.09810.742
is_sharing1.1330.0569.464
iss_source 1.417 0.03510.163
known_clinical_oncogenes0.0120.0000.012
mandatory_IS_vars0.0900.0090.099
matching_options0.0000.0000.001
outlier_filter0.1610.0110.173
outliers_by_pool_fragments0.1690.0070.176
pcr_id_column0.0200.0010.020
purity_filter0.3080.0050.313
quantification_types000
realign_after_collisions1.3630.0447.867
reduced_AF_columns0.0400.0000.041
refGene_table_cols0.0000.0000.001
remove_collisions1.2740.0297.817
reset_mandatory_IS_vars0.0040.0000.005
sample_statistics0.3030.0500.353
separate_quant_matrices0.0210.0030.025
set_mandatory_IS_vars0.0920.0040.096
set_matrix_file_suffixes0.0190.0010.020
sharing_heatmap 1.900 0.06711.301
sharing_venn 2.565 0.15537.287
threshold_filter0.0010.0000.001
top_abund_tableGrob0.6390.0130.655
top_cis_overtime_heatmap 2.044 0.09910.600
top_integrations0.0290.0030.033
top_targeted_genes0.4250.0210.446
transform_columns0.0230.0010.023