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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 1061/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.14.0  (landing page)
Giulia Pais
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: RELEASE_3_19
git_last_commit: 5effb43
git_last_commit_date: 2024-04-30 11:26:39 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 palomino3

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: 1.14.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ISAnalytics_1.14.0.tar.gz
StartedAt: 2024-06-17 05:33:02 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 05:52:20 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 1158.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ISAnalytics_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ISAnalytics/DESCRIPTION' ... OK
* this is package 'ISAnalytics' version '1.14.0'
* 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 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      2.86   0.06   17.40
import_parallel_Vispa2Matrices 2.22   0.28   38.04
CIS_grubbs_overtime            1.09   1.12   19.39
import_Vispa2_stats            1.74   0.31   16.16
top_cis_overtime_heatmap       1.24   0.19   16.66
sharing_heatmap                1.22   0.01   18.20
sharing_venn                   1.00   0.14   46.42
HSC_population_plot            0.83   0.03   15.50
iss_source                     0.78   0.08   16.11
realign_after_collisions       0.69   0.03   14.50
remove_collisions              0.61   0.05   14.34
compute_near_integrations      0.58   0.08   26.60
is_sharing                     0.56   0.08   16.21
HSC_population_size_estimate   0.46   0.02   15.08
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck/00check.log'
for details.


Installation output

ISAnalytics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: F:/biocbuild/bbs-3.19-bioc/tmpdir/Rtmp2javkB/file1d3c26c210aa/2024-06-17_collision_removal_report.html
Report correctly saved
i Report saved to: F:/biocbuild/bbs-3.19-bioc/tmpdir/Rtmp2javkB/file1d3c2c585f01/2024-06-17_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
  95.76   17.98  599.45 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.070.341.44
CIS_grubbs_overtime 1.09 1.1219.39
CIS_volcano_plot1.110.131.23
HSC_population_plot 0.83 0.0315.50
HSC_population_size_estimate 0.46 0.0215.08
NGSdataExplorer000
aggregate_metadata0.160.000.16
aggregate_values_by_key0.080.010.09
annotation_issues0.010.020.03
as_sparse_matrix0.070.000.06
available_outlier_tests000
available_tags0.010.000.02
blood_lineages_default0.030.000.03
circos_genomic_density000
clinical_relevant_suspicious_genes0.020.000.02
comparison_matrix0.030.000.03
compute_abundance0.050.000.04
compute_near_integrations 0.58 0.0826.60
cumulative_count_union000
cumulative_is0.160.010.17
date_formats000
default_af_transform000
default_iss_file_prefixes000
default_meta_agg0.030.000.04
default_rec_agg_lambdas000
default_report_path0.010.100.11
default_stats1.220.291.55
enable_progress_bars0.010.030.06
export_ISA_settings0.100.020.11
fisher_scatterplot1.390.081.47
gene_frequency_fisher0.750.010.76
generate_Vispa2_launch_AF0.190.090.28
generate_blank_association_file0.010.000.02
generate_default_folder_structure0.880.240.89
import_ISA_settings0.070.110.18
import_Vispa2_stats 1.74 0.3116.16
import_association_file1.220.311.34
import_parallel_Vispa2Matrices 2.22 0.2838.04
import_single_Vispa2Matrix1.390.381.68
inspect_tags0.000.030.03
integration_alluvial_plot 2.86 0.0617.40
is_sharing 0.56 0.0816.21
iss_source 0.78 0.0816.11
known_clinical_oncogenes0.000.010.02
mandatory_IS_vars0.130.020.14
matching_options000
outlier_filter0.250.030.28
outliers_by_pool_fragments0.230.030.27
pcr_id_column0.020.000.01
purity_filter0.350.010.37
quantification_types000
realign_after_collisions 0.69 0.0314.50
reduced_AF_columns0.050.000.05
refGene_table_cols000
remove_collisions 0.61 0.0514.34
reset_mandatory_IS_vars0.050.030.08
sample_statistics0.340.050.39
separate_quant_matrices0.030.000.03
set_mandatory_IS_vars0.140.030.18
set_matrix_file_suffixes0.020.020.03
sharing_heatmap 1.22 0.0118.20
sharing_venn 1.00 0.1446.42
threshold_filter000
top_abund_tableGrob0.710.030.78
top_cis_overtime_heatmap 1.24 0.1916.66
top_integrations0.030.000.03
top_targeted_genes0.580.020.59
transform_columns0.010.000.02