Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 1051/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.16.1 (landing page) Francesco Gazzo
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
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 04:58:09 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:14:46 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 996.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ISAnalytics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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: 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 12.7.6 * 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 6.807 0.090 19.772 sharing_venn 5.093 0.248 75.647 import_parallel_Vispa2Matrices 2.963 0.210 25.302 CIS_grubbs_overtime 2.567 0.313 15.201 import_Vispa2_stats 2.184 0.196 12.601 sharing_heatmap 2.312 0.056 19.979 top_cis_overtime_heatmap 2.270 0.077 14.337 iss_source 1.368 0.052 13.930 HSC_population_plot 1.350 0.028 12.541 is_sharing 1.163 0.042 15.039 realign_after_collisions 1.051 0.029 11.558 remove_collisions 1.003 0.031 11.348 compute_near_integrations 0.908 0.033 20.466 HSC_population_size_estimate 0.878 0.021 11.877 * 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.
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)
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-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 Report correctly saved i Report saved to: /tmp/RtmpDTg4rG/file1363726e7f5d5/2024-12-20_collision_removal_report.html Report correctly saved i Report saved to: /tmp/RtmpDTg4rG/file136373874bf46/2024-12-20_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 186.320 7.293 528.951
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 2.286 | 0.108 | 2.809 | |
CIS_grubbs_overtime | 2.567 | 0.313 | 15.201 | |
CIS_volcano_plot | 3.106 | 0.033 | 3.400 | |
HSC_population_plot | 1.350 | 0.028 | 12.541 | |
HSC_population_size_estimate | 0.878 | 0.021 | 11.877 | |
NGSdataExplorer | 0.000 | 0.000 | 0.001 | |
aggregate_metadata | 0.236 | 0.010 | 0.247 | |
aggregate_values_by_key | 0.138 | 0.004 | 0.155 | |
annotation_issues | 0.061 | 0.001 | 0.062 | |
as_sparse_matrix | 0.108 | 0.002 | 0.124 | |
available_outlier_tests | 0.001 | 0.001 | 0.001 | |
available_tags | 0.046 | 0.001 | 0.054 | |
blood_lineages_default | 0.047 | 0.001 | 0.052 | |
circos_genomic_density | 0.000 | 0.001 | 0.000 | |
clinical_relevant_suspicious_genes | 0.036 | 0.001 | 0.038 | |
comparison_matrix | 0.062 | 0.001 | 0.065 | |
compute_abundance | 0.072 | 0.004 | 0.086 | |
compute_near_integrations | 0.908 | 0.033 | 20.466 | |
cumulative_count_union | 0.000 | 0.000 | 0.001 | |
cumulative_is | 0.351 | 0.006 | 0.370 | |
date_formats | 0.000 | 0.001 | 0.001 | |
default_af_transform | 0.001 | 0.001 | 0.001 | |
default_iss_file_prefixes | 0 | 0 | 0 | |
default_meta_agg | 0.035 | 0.000 | 0.036 | |
default_rec_agg_lambdas | 0.001 | 0.000 | 0.001 | |
default_report_path | 0.014 | 0.002 | 0.016 | |
default_stats | 2.064 | 0.065 | 2.434 | |
enable_progress_bars | 0.031 | 0.004 | 0.035 | |
export_ISA_settings | 0.188 | 0.015 | 0.212 | |
fisher_scatterplot | 2.711 | 0.072 | 3.054 | |
gene_frequency_fisher | 2.680 | 0.028 | 2.948 | |
generate_Vispa2_launch_AF | 0.473 | 0.027 | 0.593 | |
generate_blank_association_file | 0.028 | 0.002 | 0.032 | |
generate_default_folder_structure | 0.837 | 0.144 | 1.019 | |
import_ISA_settings | 0.141 | 0.003 | 0.154 | |
import_Vispa2_stats | 2.184 | 0.196 | 12.601 | |
import_association_file | 1.306 | 0.171 | 1.531 | |
import_parallel_Vispa2Matrices | 2.963 | 0.210 | 25.302 | |
import_single_Vispa2Matrix | 1.532 | 0.186 | 1.716 | |
inspect_tags | 0.031 | 0.001 | 0.032 | |
integration_alluvial_plot | 6.807 | 0.090 | 19.772 | |
is_sharing | 1.163 | 0.042 | 15.039 | |
iss_source | 1.368 | 0.052 | 13.930 | |
known_clinical_oncogenes | 0.021 | 0.001 | 0.025 | |
mandatory_IS_vars | 0.198 | 0.019 | 0.235 | |
matching_options | 0.001 | 0.001 | 0.001 | |
outlier_filter | 0.336 | 0.032 | 0.400 | |
outliers_by_pool_fragments | 0.328 | 0.004 | 0.358 | |
pcr_id_column | 0.041 | 0.001 | 0.045 | |
purity_filter | 0.769 | 0.010 | 0.851 | |
quantification_types | 0.000 | 0.001 | 0.001 | |
realign_after_collisions | 1.051 | 0.029 | 11.558 | |
reduced_AF_columns | 0.093 | 0.001 | 0.094 | |
refGene_table_cols | 0.000 | 0.001 | 0.002 | |
remove_collisions | 1.003 | 0.031 | 11.348 | |
reset_mandatory_IS_vars | 0.011 | 0.001 | 0.012 | |
sample_statistics | 0.844 | 0.155 | 1.067 | |
separate_quant_matrices | 0.032 | 0.003 | 0.041 | |
set_mandatory_IS_vars | 0.204 | 0.014 | 0.243 | |
set_matrix_file_suffixes | 0.036 | 0.001 | 0.042 | |
sharing_heatmap | 2.312 | 0.056 | 19.979 | |
sharing_venn | 5.093 | 0.248 | 75.647 | |
threshold_filter | 0.001 | 0.002 | 0.003 | |
top_abund_tableGrob | 1.583 | 0.014 | 1.685 | |
top_cis_overtime_heatmap | 2.270 | 0.077 | 14.337 | |
top_integrations | 0.059 | 0.002 | 0.065 | |
top_targeted_genes | 1.058 | 0.008 | 1.182 | |
transform_columns | 0.038 | 0.001 | 0.041 | |