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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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: 2025-10-13 13:40 -0400 (Mon, 13 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 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ISAnalytics
Version: 1.18.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ISAnalytics_1.18.0.tar.gz
StartedAt: 2025-10-14 10:26:03 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 10:39:22 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 798.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ISAnalytics_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 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
integration_alluvial_plot      4.627  0.280  16.011
sharing_venn                   3.772  0.245  47.401
import_parallel_Vispa2Matrices 2.575  0.200  23.742
sharing_heatmap                2.240  0.195  16.292
CIS_grubbs_overtime            2.124  0.234  10.057
import_Vispa2_stats            1.825  0.197  11.599
top_cis_overtime_heatmap       1.878  0.091  12.477
iss_source                     1.503  0.253  12.983
remove_collisions              1.002  0.505  11.213
HSC_population_plot            1.328  0.094   8.599
is_sharing                     1.196  0.118  13.642
realign_after_collisions       1.111  0.199  10.891
compute_near_integrations      1.107  0.052  13.288
HSC_population_size_estimate   0.822  0.011   7.763
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.


Installation output

ISAnalytics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
Unable to compute sharing: i In index: 1.
i With name: absolute.
Caused by error in `pm[[2]]`:
! subscript out of bounds
i Skipping
Loading required namespace: rmarkdown
Report correctly saved
i Report saved to: /home/biocbuild/tmp/RtmpEDRbxL/file12fafd37ec6640/2025-10-14_collision_removal_report.html
Report correctly saved
i Report saved to: /home/biocbuild/tmp/RtmpEDRbxL/file12fafd484fab96/2025-10-14_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
131.699   8.154 467.982 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.2290.0281.260
CIS_grubbs_overtime 2.124 0.23410.057
CIS_volcano_plot2.5310.1072.645
HSC_population_plot1.3280.0948.599
HSC_population_size_estimate0.8220.0117.763
NGSdataExplorer000
aggregate_metadata0.1510.0000.152
aggregate_values_by_key0.0910.0000.091
annotation_issues0.0380.0000.038
as_sparse_matrix0.0750.0000.076
available_outlier_tests0.0000.0000.001
available_tags0.0330.0000.033
blood_lineages_default0.0450.0040.048
circos_genomic_density000
clinical_relevant_suspicious_genes0.020.000.02
comparison_matrix0.0470.0000.048
compute_abundance0.0500.0160.066
compute_near_integrations 1.107 0.05213.288
cumulative_count_union000
cumulative_is0.2500.0120.263
date_formats0.0010.0000.000
default_af_transform0.0010.0000.001
default_iss_file_prefixes000
default_meta_agg0.0260.0000.026
default_rec_agg_lambdas0.0000.0000.001
default_report_path0.0110.0000.012
default_stats1.0610.0471.111
enable_progress_bars0.0220.0000.022
export_ISA_settings0.1330.0000.133
fisher_scatterplot2.1360.0592.200
gene_frequency_fisher1.2590.0961.357
generate_Vispa2_launch_AF0.2730.0090.281
generate_blank_association_file0.0190.0000.019
generate_default_folder_structure0.5330.1130.647
import_ISA_settings0.1040.0000.105
import_Vispa2_stats 1.825 0.19711.599
import_association_file0.7740.1220.897
import_parallel_Vispa2Matrices 2.575 0.20023.742
import_single_Vispa2Matrix1.1110.1961.311
inspect_tags0.0180.0000.018
integration_alluvial_plot 4.627 0.28016.011
is_sharing 1.196 0.11813.642
iss_source 1.503 0.25312.983
known_clinical_oncogenes0.020.000.02
mandatory_IS_vars0.1360.0160.153
matching_options000
outlier_filter0.2190.0750.295
outliers_by_pool_fragments0.2770.0560.333
pcr_id_column0.0290.0080.037
purity_filter0.5650.1470.714
quantification_types000
realign_after_collisions 1.111 0.19910.891
reduced_AF_columns0.0610.0080.069
refGene_table_cols000
remove_collisions 1.002 0.50511.213
reset_mandatory_IS_vars0.0080.0000.008
sample_statistics0.4760.0590.537
separate_quant_matrices0.0170.0040.021
set_mandatory_IS_vars0.1660.0000.166
set_matrix_file_suffixes0.0280.0000.029
sharing_heatmap 2.240 0.19516.292
sharing_venn 3.772 0.24547.401
threshold_filter0.0010.0000.000
top_abund_tableGrob0.9730.0000.976
top_cis_overtime_heatmap 1.878 0.09112.477
top_integrations0.040.000.04
top_targeted_genes0.6390.0000.641
transform_columns0.0270.0000.027