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This page was generated on 2025-10-08 12:51 -0400 (Wed, 08 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 1072/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.19.3  (landing page)
Francesco Gazzo
Snapshot Date: 2025-10-07 13:45 -0400 (Tue, 07 Oct 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  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ISAnalytics on lconway

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: 2025-10-07 22:29:12 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 22:41:01 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 708.9 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: 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 ‘1.19.3’
* 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
integration_alluvial_plot      3.953  0.126  12.346
import_parallel_Vispa2Matrices 2.960  0.168  19.629
sharing_venn                   2.569  0.105  43.412
sharing_heatmap                2.172  0.045  13.220
CIS_grubbs_overtime            1.900  0.233   9.090
import_Vispa2_stats            1.885  0.152   9.677
top_cis_overtime_heatmap       1.881  0.064  11.551
iss_source                     1.604  0.031  12.081
HSC_population_plot            1.439  0.039   8.204
is_sharing                     1.438  0.036  11.053
realign_after_collisions       1.388  0.038   9.564
remove_collisions              1.282  0.025   9.343
HSC_population_size_estimate   1.021  0.031   7.864
compute_near_integrations      0.981  0.044  12.852
* 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-x86_64/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: 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 22:35:33.023 R[24248:483047022] XType: com.apple.fonts is not accessible.
2025-10-07 22:35:33.023 R[24248:483047022] XType: XTFontStaticRegistry is enabled.
Report correctly saved
i Report saved to: /tmp/RtmpfatGdG/file5eb81058f0a6/2025-10-07_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpfatGdG/file5eb874f09969/2025-10-07_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
117.433   5.821 403.809 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs0.9140.0480.968
CIS_grubbs_overtime1.9000.2339.090
CIS_volcano_plot1.6290.0351.671
HSC_population_plot1.4390.0398.204
HSC_population_size_estimate1.0210.0317.864
NGSdataExplorer000
aggregate_metadata0.1250.0020.128
aggregate_values_by_key0.0800.0030.086
annotation_issues0.0350.0010.036
as_sparse_matrix0.0660.0020.068
available_outlier_tests0.0000.0000.001
available_tags0.0260.0020.028
blood_lineages_default0.040.000.04
circos_genomic_density0.0000.0000.001
clinical_relevant_suspicious_genes0.0160.0010.016
comparison_matrix0.0340.0010.035
compute_abundance0.0400.0020.041
compute_near_integrations 0.981 0.04412.852
cumulative_count_union0.0000.0010.000
cumulative_is0.1970.0040.202
date_formats0.0010.0000.001
default_af_transform0.0010.0010.001
default_iss_file_prefixes000
default_meta_agg0.0160.0000.016
default_rec_agg_lambdas0.0000.0000.001
default_report_path0.0080.0010.008
default_stats1.2300.0381.275
enable_progress_bars0.0170.0030.019
export_ISA_settings0.0790.0020.081
fisher_scatterplot1.2670.0671.339
gene_frequency_fisher0.9270.0130.945
generate_Vispa2_launch_AF0.2170.0180.249
generate_blank_association_file0.0140.0010.016
generate_default_folder_structure0.8600.1070.924
import_ISA_settings0.0820.0030.085
import_Vispa2_stats1.8850.1529.677
import_association_file0.6900.1400.745
import_parallel_Vispa2Matrices 2.960 0.16819.629
import_single_Vispa2Matrix0.9860.1491.100
inspect_tags0.0160.0000.016
integration_alluvial_plot 3.953 0.12612.346
is_sharing 1.438 0.03611.053
iss_source 1.604 0.03112.081
known_clinical_oncogenes0.0140.0010.016
mandatory_IS_vars0.1100.0050.115
matching_options000
outlier_filter0.1950.0080.202
outliers_by_pool_fragments0.1880.0030.199
pcr_id_column0.0230.0000.024
purity_filter0.4390.0050.448
quantification_types000
realign_after_collisions1.3880.0389.564
reduced_AF_columns0.0600.0000.061
refGene_table_cols0.0000.0000.001
remove_collisions1.2820.0259.343
reset_mandatory_IS_vars0.0060.0010.007
sample_statistics0.3300.0580.389
separate_quant_matrices0.0170.0010.018
set_mandatory_IS_vars0.1040.0030.107
set_matrix_file_suffixes0.0230.0000.023
sharing_heatmap 2.172 0.04513.220
sharing_venn 2.569 0.10543.412
threshold_filter0.0010.0010.001
top_abund_tableGrob0.7600.0090.777
top_cis_overtime_heatmap 1.881 0.06411.551
top_integrations0.0340.0010.035
top_targeted_genes0.5140.0060.523
transform_columns0.0260.0000.028