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This page was generated on 2024-12-23 12:07 -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 kjohnson1

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: /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_1.16.1.tar.gz
StartedAt: 2024-12-20 23:02:59 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 23:10:54 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 475.3 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_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ... 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
integration_alluvial_plot      2.791  0.051   8.830
import_parallel_Vispa2Matrices 1.908  0.165  13.480
CIS_grubbs_overtime            1.645  0.178   7.347
sharing_venn                   1.411  0.089  32.476
top_cis_overtime_heatmap       1.410  0.049   7.209
import_Vispa2_stats            1.119  0.100   6.125
sharing_heatmap                1.140  0.025   8.972
HSC_population_plot            0.818  0.021   6.127
realign_after_collisions       0.814  0.018   5.874
iss_source                     0.785  0.025   6.477
remove_collisions              0.751  0.029   5.779
is_sharing                     0.745  0.019   7.466
compute_near_integrations      0.653  0.020  10.007
HSC_population_size_estimate   0.561  0.016   5.805
* 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-3.20-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/4.4-arm64/Resources/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: aarch64-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
2024-12-20 23:07:26.441 R[75848:80157478] XType: Using static font registry.
Report correctly saved
i Report saved to: /tmp/RtmpZ5kDnC/file128486fb9979b/2024-12-20_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpZ5kDnC/file1284872023fef/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 
 87.095   4.358 253.693 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.1150.0411.156
CIS_grubbs_overtime1.6450.1787.347
CIS_volcano_plot1.3740.0241.432
HSC_population_plot0.8180.0216.127
HSC_population_size_estimate0.5610.0165.805
NGSdataExplorer0.0000.0000.001
aggregate_metadata0.1050.0040.110
aggregate_values_by_key0.0710.0030.074
annotation_issues0.0290.0010.030
as_sparse_matrix0.0520.0020.054
available_outlier_tests000
available_tags0.0180.0010.018
blood_lineages_default0.0180.0010.018
circos_genomic_density000
clinical_relevant_suspicious_genes0.0100.0010.011
comparison_matrix0.0320.0010.034
compute_abundance0.0380.0020.039
compute_near_integrations 0.653 0.02010.007
cumulative_count_union000
cumulative_is0.1640.0050.180
date_formats0.0000.0000.001
default_af_transform0.0000.0000.001
default_iss_file_prefixes000
default_meta_agg0.0150.0000.015
default_rec_agg_lambdas0.0010.0000.001
default_report_path0.0090.0010.009
default_stats1.1930.0431.237
enable_progress_bars0.0180.0020.020
export_ISA_settings0.0710.0050.077
fisher_scatterplot1.1180.0271.147
gene_frequency_fisher1.1870.0181.234
generate_Vispa2_launch_AF0.1950.0180.215
generate_blank_association_file0.0080.0010.017
generate_default_folder_structure0.2420.0870.303
import_ISA_settings0.0300.0010.032
import_Vispa2_stats1.1190.1006.125
import_association_file0.6020.1330.674
import_parallel_Vispa2Matrices 1.908 0.16513.480
import_single_Vispa2Matrix1.0090.1551.088
inspect_tags0.0130.0010.013
integration_alluvial_plot2.7910.0518.830
is_sharing0.7450.0197.466
iss_source0.7850.0256.477
known_clinical_oncogenes0.0110.0010.011
mandatory_IS_vars0.0800.0080.087
matching_options000
outlier_filter0.1610.0110.173
outliers_by_pool_fragments0.1340.0010.136
pcr_id_column0.0190.0000.020
purity_filter0.3300.0040.334
quantification_types0.0010.0000.000
realign_after_collisions0.8140.0185.874
reduced_AF_columns0.0410.0000.041
refGene_table_cols000
remove_collisions0.7510.0295.779
reset_mandatory_IS_vars0.0060.0000.007
sample_statistics0.3020.0410.343
separate_quant_matrices0.0220.0010.022
set_mandatory_IS_vars0.0980.0040.101
set_matrix_file_suffixes0.0180.0010.019
sharing_heatmap1.1400.0258.972
sharing_venn 1.411 0.08932.476
threshold_filter0.0000.0010.001
top_abund_tableGrob0.6470.0090.656
top_cis_overtime_heatmap1.4100.0497.209
top_integrations0.0290.0010.030
top_targeted_genes0.3640.0040.368
transform_columns0.0170.0000.018