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This page was generated on 2025-10-02 11:38 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 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 1070/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.18.0  (landing page)
Francesco Gazzo
Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 Sep 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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ISAnalytics_1.18.0.tar.gz
StartedAt: 2025-10-02 00:20:21 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 00:30:19 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 597.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ISAnalytics_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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
sharing_venn                   4.107  0.861  32.492
integration_alluvial_plot      3.686  0.250   8.745
import_parallel_Vispa2Matrices 2.863  0.240  16.320
top_cis_overtime_heatmap       2.181  0.297   8.929
sharing_heatmap                2.304  0.158  11.437
CIS_grubbs_overtime            1.709  0.371   7.640
import_Vispa2_stats            1.685  0.232   8.029
is_sharing                     1.522  0.114   8.922
iss_source                     1.531  0.092   8.625
realign_after_collisions       1.367  0.145   7.225
HSC_population_plot            1.347  0.095   6.469
remove_collisions              1.208  0.054   6.867
compute_near_integrations      0.890  0.014   6.066
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.21-bioc/R/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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 version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
Loading required namespace: rmarkdown
Report correctly saved
i Report saved to: /tmp/Rtmp5u2wTN/file2193e229cfbc2b/2025-10-02_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/Rtmp5u2wTN/file2193e2373eb39b/2025-10-02_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
101.831   6.187 285.821 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs0.7740.0390.814
CIS_grubbs_overtime1.7090.3717.640
CIS_volcano_plot1.5500.0381.589
HSC_population_plot1.3470.0956.469
HSC_population_size_estimate1.0700.0864.104
NGSdataExplorer0.0010.0000.000
aggregate_metadata0.0990.0000.100
aggregate_values_by_key0.0650.0010.066
annotation_issues0.0260.0030.028
as_sparse_matrix0.0480.0020.051
available_outlier_tests0.0000.0000.001
available_tags0.0210.0000.022
blood_lineages_default0.0260.0000.027
circos_genomic_density000
clinical_relevant_suspicious_genes0.0110.0000.011
comparison_matrix0.0250.0030.027
compute_abundance0.0350.0010.036
compute_near_integrations0.8900.0146.066
cumulative_count_union000
cumulative_is0.1690.0220.192
date_formats0.0000.0010.000
default_af_transform0.0000.0000.001
default_iss_file_prefixes000
default_meta_agg0.0150.0030.019
default_rec_agg_lambdas0.0010.0000.001
default_report_path0.0070.0020.010
default_stats1.0860.0621.150
enable_progress_bars0.0150.0010.016
export_ISA_settings0.0680.0060.074
fisher_scatterplot1.0920.1151.207
gene_frequency_fisher0.8710.0300.901
generate_Vispa2_launch_AF0.1780.0200.196
generate_blank_association_file0.0150.0020.017
generate_default_folder_structure0.3640.1020.466
import_ISA_settings0.0620.0020.064
import_Vispa2_stats1.6850.2328.029
import_association_file0.5260.1030.629
import_parallel_Vispa2Matrices 2.863 0.24016.320
import_single_Vispa2Matrix0.8800.1431.022
inspect_tags0.0120.0000.013
integration_alluvial_plot3.6860.2508.745
is_sharing1.5220.1148.922
iss_source1.5310.0928.625
known_clinical_oncogenes0.0100.0050.014
mandatory_IS_vars0.0840.0080.091
matching_options000
outlier_filter0.1320.0160.147
outliers_by_pool_fragments0.1520.0090.162
pcr_id_column0.0180.0010.019
purity_filter0.3090.0520.362
quantification_types000
realign_after_collisions1.3670.1457.225
reduced_AF_columns0.0420.0010.043
refGene_table_cols000
remove_collisions1.2080.0546.867
reset_mandatory_IS_vars0.0020.0030.006
sample_statistics0.2950.0450.340
separate_quant_matrices0.0160.0010.017
set_mandatory_IS_vars0.0910.0020.094
set_matrix_file_suffixes0.0180.0000.019
sharing_heatmap 2.304 0.15811.437
sharing_venn 4.107 0.86132.492
threshold_filter000
top_abund_tableGrob0.6210.0290.650
top_cis_overtime_heatmap2.1810.2978.929
top_integrations0.0280.0060.034
top_targeted_genes0.4680.0600.529
transform_columns0.0190.0030.022