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This page was generated on 2025-09-22 11:41 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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: 2025-09-18 13:40 -0400 (Thu, 18 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 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: 2025-09-19 11:06:22 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 11:18:33 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 731.9 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      4.416  0.307  14.148
sharing_venn                   3.789  0.221  45.148
import_parallel_Vispa2Matrices 2.615  0.368  21.803
CIS_grubbs_overtime            2.051  0.267   8.884
import_Vispa2_stats            1.774  0.172  10.502
top_cis_overtime_heatmap       1.868  0.074  11.526
sharing_heatmap                1.789  0.115  13.938
iss_source                     1.198  0.102  10.934
HSC_population_plot            1.158  0.081   7.252
compute_near_integrations      1.122  0.074  11.791
is_sharing                     1.069  0.075  11.767
realign_after_collisions       0.973  0.077   9.385
remove_collisions              0.964  0.069   9.320
HSC_population_size_estimate   0.828  0.016   7.000
* 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
Loading required namespace: rmarkdown
Report correctly saved
i Report saved to: /home/biocbuild/tmp/RtmpqRT6Qa/file29510a5caee936/2025-09-19_collision_removal_report.html
Report correctly saved
i Report saved to: /home/biocbuild/tmp/RtmpqRT6Qa/file29510a7601cc5a/2025-09-19_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
134.096   9.231 432.863 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.3950.0481.446
CIS_grubbs_overtime2.0510.2678.884
CIS_volcano_plot1.8800.1402.023
HSC_population_plot1.1580.0817.252
HSC_population_size_estimate0.8280.0167.000
NGSdataExplorer000
aggregate_metadata0.1740.0230.199
aggregate_values_by_key0.1050.0000.106
annotation_issues0.0410.0000.041
as_sparse_matrix0.0770.0040.081
available_outlier_tests0.0010.0000.000
available_tags0.0430.0000.043
blood_lineages_default0.0340.0000.034
circos_genomic_density000
clinical_relevant_suspicious_genes0.0200.0000.021
comparison_matrix0.0470.0000.048
compute_abundance0.0550.0000.055
compute_near_integrations 1.122 0.07411.791
cumulative_count_union000
cumulative_is0.2440.0120.256
date_formats0.0010.0000.000
default_af_transform0.0000.0000.001
default_iss_file_prefixes0.0000.0000.001
default_meta_agg0.0240.0000.025
default_rec_agg_lambdas0.0000.0000.001
default_report_path0.0090.0000.010
default_stats1.4040.1161.523
enable_progress_bars0.0190.0020.022
export_ISA_settings0.1070.0000.107
fisher_scatterplot1.8810.0361.920
gene_frequency_fisher1.3050.0161.324
generate_Vispa2_launch_AF0.2650.0200.284
generate_blank_association_file0.0190.0000.020
generate_default_folder_structure0.5120.1140.627
import_ISA_settings0.1050.0000.106
import_Vispa2_stats 1.774 0.17210.502
import_association_file0.8610.1360.998
import_parallel_Vispa2Matrices 2.615 0.36821.803
import_single_Vispa2Matrix1.2360.2561.495
inspect_tags0.0190.0000.020
integration_alluvial_plot 4.416 0.30714.148
is_sharing 1.069 0.07511.767
iss_source 1.198 0.10210.934
known_clinical_oncogenes0.0150.0000.016
mandatory_IS_vars0.1400.0120.153
matching_options000
outlier_filter0.1930.0160.210
outliers_by_pool_fragments0.2250.0040.230
pcr_id_column0.0230.0040.027
purity_filter0.4700.0280.499
quantification_types000
realign_after_collisions0.9730.0779.385
reduced_AF_columns0.0620.0040.066
refGene_table_cols0.0010.0000.001
remove_collisions0.9640.0699.320
reset_mandatory_IS_vars0.0070.0000.007
sample_statistics0.4240.0430.470
separate_quant_matrices0.0200.0010.020
set_mandatory_IS_vars0.1440.0000.144
set_matrix_file_suffixes0.0270.0000.026
sharing_heatmap 1.789 0.11513.938
sharing_venn 3.789 0.22145.148
threshold_filter000
top_abund_tableGrob1.0620.0041.068
top_cis_overtime_heatmap 1.868 0.07411.526
top_integrations0.0370.0000.038
top_targeted_genes0.6320.0000.635
transform_columns0.0410.0000.041