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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1030/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.15.0  (landing page)
Giulia Pais
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: devel
git_last_commit: 2ca4cc4
git_last_commit_date: 2024-04-30 11:26:39 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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 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: 1.15.0
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_1.15.0.tar.gz
StartedAt: 2024-06-10 05:12:05 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 05:30:45 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 1120.0 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-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 Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* this is package ‘ISAnalytics’ version ‘1.15.0’
* 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
integration_alluvial_plot      7.023  0.101  21.827
sharing_venn                   5.463  0.262  83.568
import_parallel_Vispa2Matrices 3.070  0.219  28.882
CIS_grubbs_overtime            2.455  0.312  16.053
sharing_heatmap                2.435  0.054  21.768
import_Vispa2_stats            2.220  0.205  14.334
top_cis_overtime_heatmap       2.176  0.078  15.593
iss_source                     1.433  0.059  15.335
HSC_population_plot            1.414  0.031  14.242
is_sharing                     1.213  0.042  17.506
realign_after_collisions       1.070  0.030  12.025
remove_collisions              1.054  0.026  11.949
HSC_population_size_estimate   0.903  0.027  13.544
compute_near_integrations      0.887  0.032  22.308
* 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-x86_64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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
2024-06-10 05:22:36.880 R[50738:479950803] XType: com.apple.fonts is not accessible.
2024-06-10 05:22:36.881 R[50738:479950803] XType: XTFontStaticRegistry is enabled.
Report correctly saved
i Report saved to: /tmp/RtmpSkgD67/filec63222fb7310/2024-06-10_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpSkgD67/filec63213eb4db1/2024-06-10_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
193.384   7.552 599.828 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs2.3390.1192.891
CIS_grubbs_overtime 2.455 0.31216.053
CIS_volcano_plot3.2100.0433.755
HSC_population_plot 1.414 0.03114.242
HSC_population_size_estimate 0.903 0.02713.544
NGSdataExplorer0.0000.0000.001
aggregate_metadata0.2460.0040.254
aggregate_values_by_key0.1580.0040.182
annotation_issues0.0630.0020.076
as_sparse_matrix0.1140.0020.137
available_outlier_tests0.0000.0010.001
available_tags0.0540.0010.066
blood_lineages_default0.0560.0010.069
circos_genomic_density0.0000.0010.001
clinical_relevant_suspicious_genes0.0410.0010.052
comparison_matrix0.0680.0020.084
compute_abundance0.0740.0040.097
compute_near_integrations 0.887 0.03222.308
cumulative_count_union0.0010.0000.001
cumulative_is0.3730.0060.403
date_formats0.0010.0010.001
default_af_transform0.0010.0010.002
default_iss_file_prefixes0.0000.0010.000
default_meta_agg0.0390.0010.047
default_rec_agg_lambdas0.0010.0010.003
default_report_path0.0150.0020.019
default_stats2.1120.0762.523
enable_progress_bars0.0300.0030.040
export_ISA_settings0.1880.0110.244
fisher_scatterplot2.6720.0753.292
gene_frequency_fisher2.6310.0393.199
generate_Vispa2_launch_AF0.4760.0270.611
generate_blank_association_file0.0290.0010.039
generate_default_folder_structure0.8540.1481.241
import_ISA_settings0.1410.0030.169
import_Vispa2_stats 2.220 0.20514.334
import_association_file1.3730.1741.705
import_parallel_Vispa2Matrices 3.070 0.21928.882
import_single_Vispa2Matrix1.5900.1852.026
inspect_tags0.0310.0010.035
integration_alluvial_plot 7.023 0.10121.827
is_sharing 1.213 0.04217.506
iss_source 1.433 0.05915.335
known_clinical_oncogenes0.0250.0020.031
mandatory_IS_vars0.2320.0290.309
matching_options0.0000.0010.000
outlier_filter0.3460.0250.431
outliers_by_pool_fragments0.3750.0050.447
pcr_id_column0.0410.0000.047
purity_filter0.8040.0110.911
quantification_types000
realign_after_collisions 1.070 0.03012.025
reduced_AF_columns0.1020.0000.103
refGene_table_cols0.0010.0000.001
remove_collisions 1.054 0.02611.949
reset_mandatory_IS_vars0.0120.0010.013
sample_statistics0.8630.1501.106
separate_quant_matrices0.0310.0030.042
set_mandatory_IS_vars0.2260.0100.273
set_matrix_file_suffixes0.0400.0010.056
sharing_heatmap 2.435 0.05421.768
sharing_venn 5.463 0.26283.568
threshold_filter0.0000.0020.003
top_abund_tableGrob1.6040.0141.836
top_cis_overtime_heatmap 2.176 0.07815.593
top_integrations0.0640.0020.087
top_targeted_genes1.1450.0081.423
transform_columns0.0430.0010.047