Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-12 17:39 -0400 (Fri, 12 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 1061/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.14.0 (landing page) Giulia Pais
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.14.0 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ISAnalytics_1.14.0.tar.gz |
StartedAt: 2024-07-12 01:29:45 -0400 (Fri, 12 Jul 2024) |
EndedAt: 2024-07-12 01:39:18 -0400 (Fri, 12 Jul 2024) |
EllapsedTime: 572.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ISAnalytics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ISAnalytics_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck' * using R version 4.4.1 (2024-06-14 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 3.89 0.04 10.45 import_parallel_Vispa2Matrices 2.34 0.42 18.97 import_Vispa2_stats 1.84 0.31 7.61 top_cis_overtime_heatmap 1.47 0.07 7.28 sharing_heatmap 1.28 0.04 10.06 sharing_venn 1.14 0.07 38.83 CIS_grubbs_overtime 1.03 0.16 7.58 HSC_population_plot 0.90 0.02 6.95 iss_source 0.81 0.04 7.29 realign_after_collisions 0.77 0.03 6.25 is_sharing 0.75 0.04 8.57 remove_collisions 0.67 0.03 6.17 compute_near_integrations 0.60 0.02 11.27 HSC_population_size_estimate 0.52 0.02 6.11 * 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 'E:/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck/00check.log' for details.
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library 'E:/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)
ISAnalytics.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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: E:/biocbuild/bbs-3.19-bioc/tmpdir/Rtmp0WZm0g/file45804e75996/2024-07-12_collision_removal_report.html Report correctly saved i Report saved to: E:/biocbuild/bbs-3.19-bioc/tmpdir/Rtmp0WZm0g/file4580721b6998/2024-07-12_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 105.98 6.89 311.06
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 1.00 | 0.06 | 1.08 | |
CIS_grubbs_overtime | 1.03 | 0.16 | 7.58 | |
CIS_volcano_plot | 1.33 | 0.04 | 1.37 | |
HSC_population_plot | 0.90 | 0.02 | 6.95 | |
HSC_population_size_estimate | 0.52 | 0.02 | 6.11 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.14 | 0.01 | 0.16 | |
aggregate_values_by_key | 0.08 | 0.00 | 0.08 | |
annotation_issues | 0.03 | 0.02 | 0.04 | |
as_sparse_matrix | 0.05 | 0.00 | 0.05 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0.03 | 0.00 | 0.03 | |
blood_lineages_default | 0.03 | 0.00 | 0.03 | |
circos_genomic_density | 0 | 0 | 0 | |
clinical_relevant_suspicious_genes | 0 | 0 | 0 | |
comparison_matrix | 0.03 | 0.00 | 0.03 | |
compute_abundance | 0.06 | 0.00 | 0.06 | |
compute_near_integrations | 0.60 | 0.02 | 11.27 | |
cumulative_count_union | 0 | 0 | 0 | |
cumulative_is | 0.18 | 0.01 | 0.20 | |
date_formats | 0 | 0 | 0 | |
default_af_transform | 0 | 0 | 0 | |
default_iss_file_prefixes | 0 | 0 | 0 | |
default_meta_agg | 0.02 | 0.00 | 0.02 | |
default_rec_agg_lambdas | 0 | 0 | 0 | |
default_report_path | 0.00 | 0.02 | 0.01 | |
default_stats | 1.09 | 0.09 | 1.21 | |
enable_progress_bars | 0.03 | 0.02 | 0.06 | |
export_ISA_settings | 0.08 | 0.01 | 0.09 | |
fisher_scatterplot | 1.74 | 0.00 | 1.74 | |
gene_frequency_fisher | 1.01 | 0.08 | 1.09 | |
generate_Vispa2_launch_AF | 0.24 | 0.03 | 0.27 | |
generate_blank_association_file | 0.01 | 0.00 | 0.01 | |
generate_default_folder_structure | 0.80 | 0.27 | 0.92 | |
import_ISA_settings | 0.08 | 0.11 | 0.21 | |
import_Vispa2_stats | 1.84 | 0.31 | 7.61 | |
import_association_file | 1.24 | 0.28 | 1.34 | |
import_parallel_Vispa2Matrices | 2.34 | 0.42 | 18.97 | |
import_single_Vispa2Matrix | 1.33 | 0.30 | 1.59 | |
inspect_tags | 0.03 | 0.02 | 0.05 | |
integration_alluvial_plot | 3.89 | 0.04 | 10.45 | |
is_sharing | 0.75 | 0.04 | 8.57 | |
iss_source | 0.81 | 0.04 | 7.29 | |
known_clinical_oncogenes | 0.02 | 0.00 | 0.02 | |
mandatory_IS_vars | 0.09 | 0.02 | 0.11 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.25 | 0.01 | 0.26 | |
outliers_by_pool_fragments | 0.25 | 0.00 | 0.25 | |
pcr_id_column | 0.03 | 0.00 | 0.03 | |
purity_filter | 0.49 | 0.02 | 0.50 | |
quantification_types | 0 | 0 | 0 | |
realign_after_collisions | 0.77 | 0.03 | 6.25 | |
reduced_AF_columns | 0.05 | 0.00 | 0.05 | |
refGene_table_cols | 0 | 0 | 0 | |
remove_collisions | 0.67 | 0.03 | 6.17 | |
reset_mandatory_IS_vars | 0.00 | 0.08 | 0.08 | |
sample_statistics | 0.33 | 0.06 | 0.39 | |
separate_quant_matrices | 0.01 | 0.01 | 0.03 | |
set_mandatory_IS_vars | 0.13 | 0.03 | 0.16 | |
set_matrix_file_suffixes | 0.04 | 0.00 | 0.05 | |
sharing_heatmap | 1.28 | 0.04 | 10.06 | |
sharing_venn | 1.14 | 0.07 | 38.83 | |
threshold_filter | 0 | 0 | 0 | |
top_abund_tableGrob | 0.58 | 0.04 | 0.61 | |
top_cis_overtime_heatmap | 1.47 | 0.07 | 7.28 | |
top_integrations | 0.03 | 0.00 | 0.03 | |
top_targeted_genes | 0.63 | 0.00 | 0.62 | |
transform_columns | 0.03 | 0.00 | 0.04 | |