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This page was generated on 2025-08-08 12:08 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1059/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.19.3  (landing page)
Francesco Gazzo
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2025-08-07 21:48:01 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 21:59:10 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 669.9 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 (2025-06-13)
* 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      3.816  0.092  11.537
import_parallel_Vispa2Matrices 2.726  0.159  18.746
sharing_venn                   2.475  0.120  41.955
CIS_grubbs_overtime            1.924  0.247   9.072
import_Vispa2_stats            1.785  0.157   8.927
top_cis_overtime_heatmap       1.780  0.068  10.907
sharing_heatmap                1.797  0.049  12.356
iss_source                     1.350  0.032  10.990
is_sharing                     1.299  0.043  12.094
realign_after_collisions       1.212  0.037   8.297
HSC_population_plot            1.183  0.032   7.425
remove_collisions              1.184  0.024   8.104
compute_near_integrations      0.962  0.038  12.046
HSC_population_size_estimate   0.860  0.026   7.301
* 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 (2025-06-13) -- "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
2025-08-07 21:53:56.616 R[22759:407284130] XType: com.apple.fonts is not accessible.
2025-08-07 21:53:56.616 R[22759:407284130] XType: XTFontStaticRegistry is enabled.
Report correctly saved
i Report saved to: /tmp/RtmpMu6RNF/file58e765c645ff/2025-08-07_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpMu6RNF/file58e74d2261f5/2025-08-07_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
114.243   5.661 382.060 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.0600.0531.116
CIS_grubbs_overtime1.9240.2479.072
CIS_volcano_plot1.3610.0261.392
HSC_population_plot1.1830.0327.425
HSC_population_size_estimate0.8600.0267.301
NGSdataExplorer000
aggregate_metadata0.1200.0020.123
aggregate_values_by_key0.0960.0030.101
annotation_issues0.0360.0010.038
as_sparse_matrix0.0600.0020.062
available_outlier_tests000
available_tags0.0240.0000.024
blood_lineages_default0.0300.0010.030
circos_genomic_density000
clinical_relevant_suspicious_genes0.0150.0000.016
comparison_matrix0.0350.0010.036
compute_abundance0.0550.0020.057
compute_near_integrations 0.962 0.03812.046
cumulative_count_union000
cumulative_is0.1920.0040.197
date_formats000
default_af_transform0.0010.0000.001
default_iss_file_prefixes0.0000.0010.000
default_meta_agg0.0190.0000.020
default_rec_agg_lambdas0.0000.0000.001
default_report_path0.0070.0020.009
default_stats1.1560.0461.212
enable_progress_bars0.0150.0030.018
export_ISA_settings0.0800.0060.086
fisher_scatterplot1.1550.0241.186
gene_frequency_fisher1.0100.0161.038
generate_Vispa2_launch_AF0.2300.0190.260
generate_blank_association_file0.0120.0000.013
generate_default_folder_structure0.4410.0800.471
import_ISA_settings0.0690.0020.071
import_Vispa2_stats1.7850.1578.927
import_association_file0.6960.1060.740
import_parallel_Vispa2Matrices 2.726 0.15918.746
import_single_Vispa2Matrix0.9870.1271.069
inspect_tags0.0150.0000.016
integration_alluvial_plot 3.816 0.09211.537
is_sharing 1.299 0.04312.094
iss_source 1.350 0.03210.990
known_clinical_oncogenes0.0130.0010.014
mandatory_IS_vars0.1120.0040.117
matching_options000
outlier_filter0.1940.0120.208
outliers_by_pool_fragments0.2190.0070.227
pcr_id_column0.0220.0000.023
purity_filter0.3820.0040.389
quantification_types000
realign_after_collisions1.2120.0378.297
reduced_AF_columns0.0490.0010.049
refGene_table_cols0.0000.0000.001
remove_collisions1.1840.0248.104
reset_mandatory_IS_vars0.0060.0000.007
sample_statistics0.3810.0450.427
separate_quant_matrices0.0160.0010.018
set_mandatory_IS_vars0.1060.0030.110
set_matrix_file_suffixes0.0240.0010.025
sharing_heatmap 1.797 0.04912.356
sharing_venn 2.475 0.12041.955
threshold_filter0.0010.0010.000
top_abund_tableGrob0.7540.0100.767
top_cis_overtime_heatmap 1.780 0.06810.907
top_integrations0.0370.0010.038
top_targeted_genes0.5330.0070.542
transform_columns0.0240.0010.024