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This page was generated on 2025-08-23 12:03 -0400 (Sat, 23 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1061/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.19.3  (landing page)
Francesco Gazzo
Snapshot Date: 2025-08-22 13:45 -0400 (Fri, 22 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 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for ISAnalytics on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ISAnalytics_1.19.3.tar.gz
StartedAt: 2025-08-22 23:34:06 -0400 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 23:43:18 -0400 (Fri, 22 Aug 2025)
EllapsedTime: 552.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ISAnalytics_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-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 ‘1.19.3’
* 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 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                   4.124  0.260  32.661
integration_alluvial_plot      3.281  0.125   7.576
import_parallel_Vispa2Matrices 3.085  0.291  15.979
import_Vispa2_stats            1.825  0.253   7.444
sharing_heatmap                1.963  0.105  10.029
top_cis_overtime_heatmap       1.867  0.124   8.163
CIS_grubbs_overtime            1.739  0.189   6.697
iss_source                     1.441  0.050   7.593
is_sharing                     1.343  0.148   8.273
realign_after_collisions       1.250  0.107   6.606
HSC_population_plot            1.187  0.034   5.798
remove_collisions              1.148  0.023   6.587
HSC_population_size_estimate   0.965  0.058   5.555
compute_near_integrations      0.945  0.019   9.168
* 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-3.22-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.


Installation output

ISAnalytics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-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/RtmpqU654r/file2028b470f92d0a/2025-08-22_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpqU654r/file2028b45467edcf/2025-08-22_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
102.274   8.254 264.690 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs0.9880.0771.066
CIS_grubbs_overtime1.7390.1896.697
CIS_volcano_plot1.2220.0411.263
HSC_population_plot1.1870.0345.798
HSC_population_size_estimate0.9650.0585.555
NGSdataExplorer000
aggregate_metadata0.0990.0010.100
aggregate_values_by_key0.0660.0020.069
annotation_issues0.0270.0000.027
as_sparse_matrix0.0490.0000.050
available_outlier_tests000
available_tags0.0210.0000.021
blood_lineages_default0.020.000.02
circos_genomic_density000
clinical_relevant_suspicious_genes0.0110.0000.012
comparison_matrix0.0280.0000.027
compute_abundance0.0420.0000.042
compute_near_integrations0.9450.0199.168
cumulative_count_union0.0000.0000.001
cumulative_is0.1560.0000.155
date_formats000
default_af_transform000
default_iss_file_prefixes000
default_meta_agg0.0170.0000.017
default_rec_agg_lambdas0.0010.0000.000
default_report_path0.0050.0030.007
default_stats1.0150.0281.043
enable_progress_bars0.0130.0010.014
export_ISA_settings0.0650.0000.065
fisher_scatterplot0.9640.0651.029
gene_frequency_fisher0.8250.0050.831
generate_Vispa2_launch_AF0.1640.0090.173
generate_blank_association_file0.0150.0000.015
generate_default_folder_structure0.3790.1020.481
import_ISA_settings0.0720.0000.071
import_Vispa2_stats1.8250.2537.444
import_association_file0.5660.1520.716
import_parallel_Vispa2Matrices 3.085 0.29115.979
import_single_Vispa2Matrix0.8810.1441.026
inspect_tags0.0120.0000.013
integration_alluvial_plot3.2810.1257.576
is_sharing1.3430.1488.273
iss_source1.4410.0507.593
known_clinical_oncogenes0.0100.0010.011
mandatory_IS_vars0.0900.0020.092
matching_options000
outlier_filter0.1510.0060.157
outliers_by_pool_fragments0.1480.0000.148
pcr_id_column0.0190.0000.019
purity_filter0.3130.0010.314
quantification_types000
realign_after_collisions1.2500.1076.606
reduced_AF_columns0.0470.0000.047
refGene_table_cols0.0000.0000.001
remove_collisions1.1480.0236.587
reset_mandatory_IS_vars0.0050.0000.004
sample_statistics0.2900.0090.300
separate_quant_matrices0.0170.0000.018
set_mandatory_IS_vars0.1000.0000.101
set_matrix_file_suffixes0.0180.0000.018
sharing_heatmap 1.963 0.10510.029
sharing_venn 4.124 0.26032.661
threshold_filter0.0010.0000.000
top_abund_tableGrob0.6190.0210.640
top_cis_overtime_heatmap1.8670.1248.163
top_integrations0.0310.0000.031
top_targeted_genes0.4710.0170.487
transform_columns0.0180.0000.018