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This page was generated on 2025-10-13 11:41 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 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: 2025-10-09 13:40 -0400 (Thu, 09 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 12.7.5 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 kunpeng2

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.

raw results


Summary

Package: ISAnalytics
Version: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2025-10-10 10:15:39 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 10:28:57 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 797.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* 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 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
integration_alluvial_plot      4.663  0.310  16.213
sharing_venn                   3.704  0.456  45.428
import_parallel_Vispa2Matrices 2.642  0.322  24.582
sharing_heatmap                2.217  0.134  16.021
top_cis_overtime_heatmap       2.010  0.233  12.668
CIS_grubbs_overtime            1.996  0.156   9.942
import_Vispa2_stats            1.637  0.146  11.438
iss_source                     1.375  0.176  12.495
HSC_population_plot            1.328  0.028   8.292
is_sharing                     1.165  0.058  13.079
compute_near_integrations      1.099  0.059  13.450
remove_collisions              1.037  0.116  10.675
realign_after_collisions       1.037  0.103  10.718
HSC_population_size_estimate   0.821  0.036   7.733
* 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-3.21-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.


Installation output

ISAnalytics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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
Unable to compute sharing: i In index: 1.
i With name: absolute.
Caused by error in `pm[[2]]`:
! subscript out of bounds
i Skipping
Loading required namespace: rmarkdown
Report correctly saved
i Report saved to: /home/biocbuild/tmp/Rtmp3SOXjF/filece8017046d455/2025-10-10_collision_removal_report.html
Report correctly saved
i Report saved to: /home/biocbuild/tmp/Rtmp3SOXjF/filece80149c797f5/2025-10-10_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
134.096   7.905 470.277 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.1730.0281.204
CIS_grubbs_overtime1.9960.1569.942
CIS_volcano_plot2.5240.0602.587
HSC_population_plot1.3280.0288.292
HSC_population_size_estimate0.8210.0367.733
NGSdataExplorer000
aggregate_metadata0.1610.0040.165
aggregate_values_by_key0.0930.0040.098
annotation_issues0.0400.0000.041
as_sparse_matrix0.0770.0000.077
available_outlier_tests000
available_tags0.0330.0000.034
blood_lineages_default0.0400.0080.048
circos_genomic_density000
clinical_relevant_suspicious_genes0.0100.0080.019
comparison_matrix0.0390.0040.044
compute_abundance0.0480.0000.048
compute_near_integrations 1.099 0.05913.450
cumulative_count_union000
cumulative_is0.2370.0340.273
date_formats000
default_af_transform0.0010.0000.001
default_iss_file_prefixes000
default_meta_agg0.0230.0000.023
default_rec_agg_lambdas000
default_report_path0.0090.0000.009
default_stats1.0440.0321.077
enable_progress_bars0.020.000.02
export_ISA_settings0.1220.0000.122
fisher_scatterplot2.0980.0082.109
gene_frequency_fisher1.2190.0841.305
generate_Vispa2_launch_AF0.2590.0180.275
generate_blank_association_file0.0180.0000.018
generate_default_folder_structure0.4450.0830.527
import_ISA_settings0.0800.0030.084
import_Vispa2_stats 1.637 0.14611.438
import_association_file0.8480.0990.948
import_parallel_Vispa2Matrices 2.642 0.32224.582
import_single_Vispa2Matrix1.0970.2091.310
inspect_tags0.0180.0000.017
integration_alluvial_plot 4.663 0.31016.213
is_sharing 1.165 0.05813.079
iss_source 1.375 0.17612.495
known_clinical_oncogenes0.0160.0000.016
mandatory_IS_vars0.1350.0000.136
matching_options000
outlier_filter0.2160.0080.226
outliers_by_pool_fragments0.2410.0160.258
pcr_id_column0.0280.0000.028
purity_filter0.5050.0440.551
quantification_types000
realign_after_collisions 1.037 0.10310.718
reduced_AF_columns0.0610.0000.062
refGene_table_cols000
remove_collisions 1.037 0.11610.675
reset_mandatory_IS_vars0.0080.0000.008
sample_statistics0.4580.0430.504
separate_quant_matrices0.0160.0040.019
set_mandatory_IS_vars0.1520.0080.160
set_matrix_file_suffixes0.0280.0000.028
sharing_heatmap 2.217 0.13416.021
sharing_venn 3.704 0.45645.428
threshold_filter000
top_abund_tableGrob0.9880.0681.058
top_cis_overtime_heatmap 2.010 0.23312.668
top_integrations0.0530.0160.069
top_targeted_genes0.7000.0080.710
transform_columns0.0290.0000.030