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This page was generated on 2024-05-13 11:32:06 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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 1026/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.15.0 (landing page) Giulia Pais
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the ISAnalytics package: - 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: 1.15.0 |
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: 2024-05-12 17:15:44 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 17:23:39 -0400 (Sun, 12 May 2024) |
EllapsedTime: 475.3 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_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/ISAnalytics.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * 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 2.822 0.048 8.771 import_parallel_Vispa2Matrices 1.901 0.172 13.497 CIS_grubbs_overtime 1.488 0.158 7.130 sharing_venn 1.492 0.101 32.697 import_Vispa2_stats 1.320 0.159 6.393 top_cis_overtime_heatmap 1.408 0.049 7.173 sharing_heatmap 1.150 0.023 8.928 iss_source 0.867 0.028 6.814 HSC_population_plot 0.807 0.021 6.065 realign_after_collisions 0.783 0.017 5.785 is_sharing 0.757 0.022 7.423 remove_collisions 0.744 0.026 5.717 compute_near_integrations 0.634 0.020 9.994 HSC_population_size_estimate 0.545 0.022 5.814 * 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-mac-arm64/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-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)
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: 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 2024-05-12 17:20:13.341 R[32803:53741965] XType: Using static font registry. Report correctly saved i Report saved to: /tmp/RtmpdIUo3G/file802359616fe7/2024-05-12_collision_removal_report.html Report correctly saved i Report saved to: /tmp/RtmpdIUo3G/file8023531c42e9/2024-05-12_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 86.581 4.254 252.660
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 1.070 | 0.035 | 1.106 | |
CIS_grubbs_overtime | 1.488 | 0.158 | 7.130 | |
CIS_volcano_plot | 1.337 | 0.023 | 1.360 | |
HSC_population_plot | 0.807 | 0.021 | 6.065 | |
HSC_population_size_estimate | 0.545 | 0.022 | 5.814 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.108 | 0.002 | 0.111 | |
aggregate_values_by_key | 0.075 | 0.002 | 0.078 | |
annotation_issues | 0.030 | 0.001 | 0.031 | |
as_sparse_matrix | 0.056 | 0.001 | 0.057 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0.021 | 0.000 | 0.021 | |
blood_lineages_default | 0.020 | 0.001 | 0.020 | |
circos_genomic_density | 0.001 | 0.000 | 0.000 | |
clinical_relevant_suspicious_genes | 0.011 | 0.001 | 0.012 | |
comparison_matrix | 0.037 | 0.001 | 0.038 | |
compute_abundance | 0.040 | 0.002 | 0.041 | |
compute_near_integrations | 0.634 | 0.020 | 9.994 | |
cumulative_count_union | 0 | 0 | 0 | |
cumulative_is | 0.171 | 0.003 | 0.179 | |
date_formats | 0 | 0 | 0 | |
default_af_transform | 0.001 | 0.000 | 0.001 | |
default_iss_file_prefixes | 0.000 | 0.000 | 0.001 | |
default_meta_agg | 0.015 | 0.000 | 0.016 | |
default_rec_agg_lambdas | 0 | 0 | 0 | |
default_report_path | 0.009 | 0.001 | 0.009 | |
default_stats | 0.877 | 0.032 | 0.916 | |
enable_progress_bars | 0.009 | 0.002 | 0.011 | |
export_ISA_settings | 0.032 | 0.004 | 0.037 | |
fisher_scatterplot | 0.954 | 0.025 | 0.982 | |
gene_frequency_fisher | 1.330 | 0.019 | 1.351 | |
generate_Vispa2_launch_AF | 0.227 | 0.020 | 0.246 | |
generate_blank_association_file | 0.013 | 0.001 | 0.016 | |
generate_default_folder_structure | 0.402 | 0.125 | 0.453 | |
import_ISA_settings | 0.062 | 0.001 | 0.064 | |
import_Vispa2_stats | 1.320 | 0.159 | 6.393 | |
import_association_file | 0.633 | 0.140 | 0.694 | |
import_parallel_Vispa2Matrices | 1.901 | 0.172 | 13.497 | |
import_single_Vispa2Matrix | 0.974 | 0.148 | 1.048 | |
inspect_tags | 0.013 | 0.000 | 0.013 | |
integration_alluvial_plot | 2.822 | 0.048 | 8.771 | |
is_sharing | 0.757 | 0.022 | 7.423 | |
iss_source | 0.867 | 0.028 | 6.814 | |
known_clinical_oncogenes | 0.012 | 0.001 | 0.013 | |
mandatory_IS_vars | 0.095 | 0.009 | 0.105 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.186 | 0.011 | 0.197 | |
outliers_by_pool_fragments | 0.148 | 0.002 | 0.150 | |
pcr_id_column | 0.021 | 0.001 | 0.021 | |
purity_filter | 0.336 | 0.006 | 0.342 | |
quantification_types | 0.001 | 0.000 | 0.000 | |
realign_after_collisions | 0.783 | 0.017 | 5.785 | |
reduced_AF_columns | 0.042 | 0.000 | 0.043 | |
refGene_table_cols | 0.000 | 0.000 | 0.001 | |
remove_collisions | 0.744 | 0.026 | 5.717 | |
reset_mandatory_IS_vars | 0.004 | 0.001 | 0.005 | |
sample_statistics | 0.327 | 0.052 | 0.379 | |
separate_quant_matrices | 0.018 | 0.001 | 0.018 | |
set_mandatory_IS_vars | 0.096 | 0.004 | 0.102 | |
set_matrix_file_suffixes | 0.018 | 0.000 | 0.018 | |
sharing_heatmap | 1.150 | 0.023 | 8.928 | |
sharing_venn | 1.492 | 0.101 | 32.697 | |
threshold_filter | 0.000 | 0.001 | 0.001 | |
top_abund_tableGrob | 0.631 | 0.009 | 0.640 | |
top_cis_overtime_heatmap | 1.408 | 0.049 | 7.173 | |
top_integrations | 0.028 | 0.001 | 0.028 | |
top_targeted_genes | 0.352 | 0.003 | 0.354 | |
transform_columns | 0.018 | 0.001 | 0.019 | |