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This page was generated on 2025-10-13 11:39 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 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: 2025-10-09 13:40 -0400 (Thu, 09 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 12.7.5 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 merida1

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: /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_1.18.0.tar.gz
StartedAt: 2025-10-10 05:27:39 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 05:48:48 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 1269.6 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.18.0’
* 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 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                   8.065  0.343  83.781
integration_alluvial_plot      8.060  0.277  24.969
import_parallel_Vispa2Matrices 4.825  0.285  35.362
sharing_heatmap                4.082  0.108  25.360
CIS_grubbs_overtime            3.103  0.347  16.892
import_Vispa2_stats            2.989  0.229  17.277
top_cis_overtime_heatmap       2.981  0.142  21.230
iss_source                     2.489  0.077  19.001
is_sharing                     2.451  0.106  20.776
HSC_population_plot            2.402  0.078  14.940
realign_after_collisions       1.950  0.065  16.074
remove_collisions              1.850  0.055  16.241
compute_near_integrations      1.554  0.087  23.595
HSC_population_size_estimate   1.502  0.058  14.199
* 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-3.21-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 ‘1.18.0’
** 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 RC (2025-06-05 r88288) -- "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
2025-10-10 05:39:10.008 R[36369:467673734] XType: com.apple.fonts is not accessible.
2025-10-10 05:39:10.008 R[36369:467673734] XType: XTFontStaticRegistry is enabled.
Report correctly saved
i Report saved to: /tmp/RtmphcEc9y/file8e117843602e/2025-10-10_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmphcEc9y/file8e11567ddadb/2025-10-10_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
208.719   8.277 717.413 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs2.0740.0852.411
CIS_grubbs_overtime 3.103 0.34716.892
CIS_volcano_plot3.6970.0944.105
HSC_population_plot 2.402 0.07814.940
HSC_population_size_estimate 1.502 0.05814.199
NGSdataExplorer0.0000.0000.001
aggregate_metadata0.2300.0090.243
aggregate_values_by_key0.1440.0150.164
annotation_issues0.0620.0070.070
as_sparse_matrix0.1090.0070.131
available_outlier_tests0.0000.0010.000
available_tags0.0520.0020.059
blood_lineages_default0.0640.0010.083
circos_genomic_density0.0000.0000.001
clinical_relevant_suspicious_genes0.0290.0000.032
comparison_matrix0.0640.0010.069
compute_abundance0.0720.0090.091
compute_near_integrations 1.554 0.08723.595
cumulative_count_union0.0000.0010.001
cumulative_is0.3620.0160.409
date_formats0.0010.0010.002
default_af_transform0.0010.0010.002
default_iss_file_prefixes000
default_meta_agg0.0390.0000.043
default_rec_agg_lambdas0.0010.0010.002
default_report_path0.0140.0010.019
default_stats2.1600.0462.392
enable_progress_bars0.0290.0030.036
export_ISA_settings0.1760.0030.196
fisher_scatterplot2.9160.1973.410
gene_frequency_fisher2.5430.0582.827
generate_Vispa2_launch_AF0.4600.0420.555
generate_blank_association_file0.0270.0030.034
generate_default_folder_structure0.8450.1611.051
import_ISA_settings0.1380.0020.152
import_Vispa2_stats 2.989 0.22917.277
import_association_file1.3050.1831.491
import_parallel_Vispa2Matrices 4.825 0.28535.362
import_single_Vispa2Matrix1.6240.2021.928
inspect_tags0.0280.0010.030
integration_alluvial_plot 8.060 0.27724.969
is_sharing 2.451 0.10620.776
iss_source 2.489 0.07719.001
known_clinical_oncogenes0.0230.0010.026
mandatory_IS_vars0.2090.0060.236
matching_options0.0010.0000.002
outlier_filter0.3340.0190.381
outliers_by_pool_fragments0.3450.0080.383
pcr_id_column0.0390.0010.043
purity_filter0.7890.0140.889
quantification_types0.0000.0010.000
realign_after_collisions 1.950 0.06516.074
reduced_AF_columns0.1010.0010.113
refGene_table_cols0.0000.0010.002
remove_collisions 1.850 0.05516.241
reset_mandatory_IS_vars0.0110.0010.014
sample_statistics0.8240.1491.071
separate_quant_matrices0.0310.0070.041
set_mandatory_IS_vars0.1910.0050.212
set_matrix_file_suffixes0.0400.0020.046
sharing_heatmap 4.082 0.10825.360
sharing_venn 8.065 0.34383.781
threshold_filter0.0010.0020.003
top_abund_tableGrob1.5410.0241.708
top_cis_overtime_heatmap 2.981 0.14221.230
top_integrations0.0610.0020.068
top_targeted_genes1.0670.0121.135
transform_columns0.0420.0020.045