Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-09 11:39 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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: 2025-10-06 13:40 -0400 (Mon, 06 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 merida1

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: 2025-10-07 05:16:54 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 05:38:35 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 1300.7 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.18.0’
* 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
sharing_venn                   8.089  0.335  84.775
integration_alluvial_plot      8.082  0.283  25.556
import_parallel_Vispa2Matrices 4.768  0.277  35.980
sharing_heatmap                3.858  0.101  25.513
CIS_grubbs_overtime            3.118  0.352  17.272
import_Vispa2_stats            2.983  0.240  17.981
top_cis_overtime_heatmap       3.000  0.144  21.243
iss_source                     2.509  0.075  19.252
HSC_population_plot            2.379  0.071  15.424
is_sharing                     2.303  0.100  20.974
realign_after_collisions       1.947  0.059  16.306
remove_collisions              1.853  0.052  16.231
compute_near_integrations      1.573  0.077  24.114
HSC_population_size_estimate   1.512  0.061  14.535
* 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-x86_64/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 RC (2025-06-05 r88288) -- "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
2025-10-07 05:28:35.120 R[78467:457506292] XType: com.apple.fonts is not accessible.
2025-10-07 05:28:35.122 R[78467:457506292] XType: XTFontStaticRegistry is enabled.
Report correctly saved
i Report saved to: /tmp/Rtmp7JP7XO/file13283361a9d07/2025-10-07_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/Rtmp7JP7XO/file1328342e26dfb/2025-10-07_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
209.206   8.518 736.198 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs2.0870.0902.415
CIS_grubbs_overtime 3.118 0.35217.272
CIS_volcano_plot3.7030.0914.278
HSC_population_plot 2.379 0.07115.424
HSC_population_size_estimate 1.512 0.06114.535
NGSdataExplorer000
aggregate_metadata0.2320.0080.263
aggregate_values_by_key0.1420.0120.172
annotation_issues0.0600.0070.082
as_sparse_matrix0.1080.0060.124
available_outlier_tests0.0000.0010.000
available_tags0.0480.0020.052
blood_lineages_default0.0620.0020.073
circos_genomic_density000
clinical_relevant_suspicious_genes0.0280.0000.030
comparison_matrix0.0640.0010.074
compute_abundance0.0720.0090.089
compute_near_integrations 1.573 0.07724.114
cumulative_count_union0.0000.0010.001
cumulative_is0.3530.0150.405
date_formats0.0000.0010.001
default_af_transform0.0010.0000.002
default_iss_file_prefixes0.0000.0010.001
default_meta_agg0.0370.0010.042
default_rec_agg_lambdas0.0010.0000.002
default_report_path0.0140.0020.016
default_stats2.1550.0422.477
enable_progress_bars0.0290.0040.036
export_ISA_settings0.1790.0040.199
fisher_scatterplot2.8700.1913.374
gene_frequency_fisher2.5710.0532.838
generate_Vispa2_launch_AF0.4530.0470.553
generate_blank_association_file0.0290.0040.043
generate_default_folder_structure0.8300.1591.043
import_ISA_settings0.1350.0030.149
import_Vispa2_stats 2.983 0.24017.981
import_association_file1.3080.1941.620
import_parallel_Vispa2Matrices 4.768 0.27735.980
import_single_Vispa2Matrix1.5680.1951.900
inspect_tags0.0300.0000.037
integration_alluvial_plot 8.082 0.28325.556
is_sharing 2.303 0.10020.974
iss_source 2.509 0.07519.252
known_clinical_oncogenes0.0220.0000.026
mandatory_IS_vars0.2120.0060.260
matching_options000
outlier_filter0.3430.0240.413
outliers_by_pool_fragments0.3580.0090.448
pcr_id_column0.0420.0010.052
purity_filter0.7910.0191.000
quantification_types0.0000.0010.001
realign_after_collisions 1.947 0.05916.306
reduced_AF_columns0.0960.0010.104
refGene_table_cols0.0000.0010.003
remove_collisions 1.853 0.05216.231
reset_mandatory_IS_vars0.0120.0020.014
sample_statistics0.8340.1491.105
separate_quant_matrices0.0310.0050.040
set_mandatory_IS_vars0.1960.0060.224
set_matrix_file_suffixes0.0380.0010.043
sharing_heatmap 3.858 0.10125.513
sharing_venn 8.089 0.33584.775
threshold_filter0.0000.0010.002
top_abund_tableGrob1.5690.0221.675
top_cis_overtime_heatmap 3.000 0.14421.243
top_integrations0.0600.0020.067
top_targeted_genes1.1440.0111.315
transform_columns0.0450.0020.050