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This page was generated on 2025-09-20 12:06 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1069/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.19.3  (landing page)
Francesco Gazzo
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 Sep 2025)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: devel
git_last_commit: 923672f
git_last_commit_date: 2025-07-21 09:31:21 -0400 (Mon, 21 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ISAnalytics on kjohnson3

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: 1.19.3
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: 2025-09-19 20:01:43 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 20:05:16 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 213.7 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_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* 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
import_parallel_Vispa2Matrices 1.099  0.093   6.576
sharing_venn                   0.982  0.049  11.080
* 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.


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 ‘1.19.3’
** 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)

Tests output

ISAnalytics.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "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
2025-09-19 20:03:38.165 R[93720:280609949] XType: Using static font registry.
Report correctly saved
i Report saved to: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpsy0sN5/file16e185f9eb207/2025-09-19_collision_removal_report.html
Report correctly saved
i Report saved to: /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmpsy0sN5/file16e186d357317/2025-09-19_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
 34.080   1.883 119.253 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs0.3080.0140.323
CIS_grubbs_overtime0.7600.0663.029
CIS_volcano_plot0.5210.0110.532
HSC_population_plot0.4820.0152.460
HSC_population_size_estimate0.3500.0122.376
NGSdataExplorer000
aggregate_metadata0.0300.0010.030
aggregate_values_by_key0.0210.0010.021
annotation_issues0.0090.0000.009
as_sparse_matrix0.0170.0010.017
available_outlier_tests000
available_tags0.0060.0000.007
blood_lineages_default0.0090.0000.009
circos_genomic_density000
clinical_relevant_suspicious_genes0.0030.0000.004
comparison_matrix0.0080.0000.008
compute_abundance0.0120.0010.012
compute_near_integrations0.3830.0173.916
cumulative_count_union000
cumulative_is0.0480.0010.049
date_formats000
default_af_transform0.0010.0000.000
default_iss_file_prefixes000
default_meta_agg0.0040.0000.005
default_rec_agg_lambdas0.0010.0000.000
default_report_path0.0020.0000.003
default_stats0.4740.0110.492
enable_progress_bars0.0060.0010.007
export_ISA_settings0.0230.0010.024
fisher_scatterplot0.3780.0160.395
gene_frequency_fisher0.2890.0030.293
generate_Vispa2_launch_AF0.0670.0080.080
generate_blank_association_file0.0050.0010.005
generate_default_folder_structure0.3130.0640.336
import_ISA_settings0.0180.0010.020
import_Vispa2_stats0.6630.0883.098
import_association_file0.1920.0700.239
import_parallel_Vispa2Matrices1.0990.0936.576
import_single_Vispa2Matrix0.3680.0730.401
inspect_tags0.0030.0000.003
integration_alluvial_plot1.2240.0413.928
is_sharing0.5560.0173.507
iss_source0.5580.0123.349
known_clinical_oncogenes0.0030.0000.003
mandatory_IS_vars0.0260.0020.027
matching_options0.0000.0000.001
outlier_filter0.0470.0030.059
outliers_by_pool_fragments0.0440.0000.044
pcr_id_column0.0050.0000.005
purity_filter0.0950.0010.096
quantification_types000
realign_after_collisions0.4990.0152.925
reduced_AF_columns0.0140.0000.016
refGene_table_cols0.0000.0000.001
remove_collisions0.4690.0082.873
reset_mandatory_IS_vars0.0020.0000.001
sample_statistics0.0930.0150.108
separate_quant_matrices0.0060.0000.006
set_mandatory_IS_vars0.0260.0020.036
set_matrix_file_suffixes0.0050.0010.006
sharing_heatmap0.6910.0243.937
sharing_venn 0.982 0.04911.080
threshold_filter0.0000.0000.001
top_abund_tableGrob0.1950.0020.197
top_cis_overtime_heatmap0.7420.0293.782
top_integrations0.0110.0010.012
top_targeted_genes0.1290.0060.135
transform_columns0.0050.0000.006