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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1051/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.16.1  (landing page)
Francesco Gazzo
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: RELEASE_3_20
git_last_commit: 38a25cb
git_last_commit_date: 2024-12-05 05:11:34 -0500 (Thu, 05 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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


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: 1.16.1
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ISAnalytics_1.16.1.tar.gz
StartedAt: 2024-12-20 01:32:53 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:44:52 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 719.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ISAnalytics_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* this is package ‘ISAnalytics’ version ‘1.16.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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      2.728  0.073   7.266
sharing_venn                   2.032  0.159  26.559
import_parallel_Vispa2Matrices 1.530  0.183  10.103
CIS_grubbs_overtime            1.259  0.095   5.810
top_cis_overtime_heatmap       1.228  0.089   5.598
sharing_heatmap                1.150  0.031   7.457
iss_source                     0.720  0.059   5.306
is_sharing                     0.662  0.065   5.811
compute_near_integrations      0.580  0.018   7.569
* 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-3.20-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.


Installation output

ISAnalytics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ISAnalytics’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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: /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpnUfyQh/file32ca43177d84be/2024-12-20_collision_removal_report.html
Report correctly saved
i Report saved to: /home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpnUfyQh/file32ca43690755f/2024-12-20_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 834 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
 82.134   4.795 217.266 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs0.9540.1461.101
CIS_grubbs_overtime1.2590.0955.810
CIS_volcano_plot1.1030.0521.156
HSC_population_plot0.7320.0134.842
HSC_population_size_estimate0.4600.0054.545
NGSdataExplorer000
aggregate_metadata0.0880.0000.088
aggregate_values_by_key0.0580.0010.059
annotation_issues0.0250.0000.025
as_sparse_matrix0.0450.0170.062
available_outlier_tests0.0000.0000.001
available_tags0.0190.0040.023
blood_lineages_default0.0190.0020.021
circos_genomic_density000
clinical_relevant_suspicious_genes0.0100.0010.011
comparison_matrix0.0330.0060.038
compute_abundance0.0320.0010.034
compute_near_integrations0.5800.0187.569
cumulative_count_union000
cumulative_is0.140.000.14
date_formats0.0010.0000.000
default_af_transform000
default_iss_file_prefixes000
default_meta_agg0.0130.0000.013
default_rec_agg_lambdas0.0000.0000.001
default_report_path0.0060.0000.006
default_stats0.8760.0250.901
enable_progress_bars0.0120.0010.013
export_ISA_settings0.0620.0030.065
fisher_scatterplot1.1750.0311.206
gene_frequency_fisher0.8010.0440.845
generate_Vispa2_launch_AF0.1540.0100.163
generate_blank_association_file0.0110.0000.011
generate_default_folder_structure0.2940.0680.363
import_ISA_settings0.0530.0000.053
import_Vispa2_stats1.0010.1274.955
import_association_file0.4490.1040.555
import_parallel_Vispa2Matrices 1.530 0.18310.103
import_single_Vispa2Matrix0.6820.0810.759
inspect_tags0.0120.0000.012
integration_alluvial_plot2.7280.0737.266
is_sharing0.6620.0655.811
iss_source0.7200.0595.306
known_clinical_oncogenes0.0080.0010.011
mandatory_IS_vars0.0720.0130.086
matching_options000
outlier_filter0.1340.0110.145
outliers_by_pool_fragments0.1230.0010.125
pcr_id_column0.0160.0010.016
purity_filter0.2880.0010.289
quantification_types000
realign_after_collisions0.6870.0584.418
reduced_AF_columns0.0420.0000.042
refGene_table_cols000
remove_collisions0.6900.0324.549
reset_mandatory_IS_vars0.0060.0010.007
sample_statistics0.2820.0030.285
separate_quant_matrices0.0130.0010.015
set_mandatory_IS_vars0.0800.0010.081
set_matrix_file_suffixes0.0150.0000.015
sharing_heatmap1.1500.0317.457
sharing_venn 2.032 0.15926.559
threshold_filter000
top_abund_tableGrob0.5690.0370.605
top_cis_overtime_heatmap1.2280.0895.598
top_integrations0.0230.0010.024
top_targeted_genes0.4210.0160.437
transform_columns0.0170.0000.017