Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-28 17:40 -0400 (Fri, 28 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
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 | ![]() | ||||||||
palomino3 | 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 | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ISAnalytics_1.14.0.tar.gz |
StartedAt: 2024-06-27 00:22:20 -0400 (Thu, 27 Jun 2024) |
EndedAt: 2024-06-27 00:31:31 -0400 (Thu, 27 Jun 2024) |
EllapsedTime: 551.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ISAnalytics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ISAnalytics_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 loading without being on the library search path ... 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 2.697 0.097 8.121 sharing_venn 2.121 0.217 29.565 import_parallel_Vispa2Matrices 1.746 0.207 12.369 CIS_grubbs_overtime 1.250 0.092 6.164 top_cis_overtime_heatmap 1.194 0.121 6.238 sharing_heatmap 1.181 0.123 8.344 import_Vispa2_stats 1.072 0.181 5.548 iss_source 0.819 0.072 6.191 HSC_population_plot 0.758 0.045 5.618 is_sharing 0.715 0.053 6.839 remove_collisions 0.641 0.067 5.318 realign_after_collisions 0.610 0.080 5.208 compute_near_integrations 0.591 0.005 8.458 HSC_population_size_estimate 0.476 0.008 5.043 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck/00check.log’ for details.
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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/Rtmp1WPtTL/file1fed6210bb04b9/2024-06-27_collision_removal_report.html Report correctly saved i Report saved to: /tmp/Rtmp1WPtTL/file1fed624b90017e/2024-06-27_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 82.382 4.576 233.451
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 0.949 | 0.060 | 1.010 | |
CIS_grubbs_overtime | 1.250 | 0.092 | 6.164 | |
CIS_volcano_plot | 1.163 | 0.056 | 1.219 | |
HSC_population_plot | 0.758 | 0.045 | 5.618 | |
HSC_population_size_estimate | 0.476 | 0.008 | 5.043 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.106 | 0.012 | 0.118 | |
aggregate_values_by_key | 0.068 | 0.012 | 0.080 | |
annotation_issues | 0.028 | 0.000 | 0.027 | |
as_sparse_matrix | 0.05 | 0.00 | 0.05 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0.021 | 0.000 | 0.021 | |
blood_lineages_default | 0.021 | 0.000 | 0.020 | |
circos_genomic_density | 0.001 | 0.000 | 0.000 | |
clinical_relevant_suspicious_genes | 0.008 | 0.004 | 0.011 | |
comparison_matrix | 0.033 | 0.000 | 0.032 | |
compute_abundance | 0.030 | 0.004 | 0.033 | |
compute_near_integrations | 0.591 | 0.005 | 8.458 | |
cumulative_count_union | 0.000 | 0.001 | 0.000 | |
cumulative_is | 0.183 | 0.019 | 0.202 | |
date_formats | 0.000 | 0.001 | 0.001 | |
default_af_transform | 0.000 | 0.001 | 0.001 | |
default_iss_file_prefixes | 0.000 | 0.000 | 0.001 | |
default_meta_agg | 0.007 | 0.009 | 0.017 | |
default_rec_agg_lambdas | 0.001 | 0.000 | 0.000 | |
default_report_path | 0.009 | 0.000 | 0.008 | |
default_stats | 0.976 | 0.060 | 1.035 | |
enable_progress_bars | 0.016 | 0.000 | 0.015 | |
export_ISA_settings | 0.073 | 0.000 | 0.073 | |
fisher_scatterplot | 1.293 | 0.071 | 1.364 | |
gene_frequency_fisher | 0.820 | 0.004 | 0.824 | |
generate_Vispa2_launch_AF | 0.173 | 0.012 | 0.202 | |
generate_blank_association_file | 0.013 | 0.000 | 0.013 | |
generate_default_folder_structure | 0.352 | 0.058 | 0.385 | |
import_ISA_settings | 0.053 | 0.017 | 0.069 | |
import_Vispa2_stats | 1.072 | 0.181 | 5.548 | |
import_association_file | 0.586 | 0.097 | 0.647 | |
import_parallel_Vispa2Matrices | 1.746 | 0.207 | 12.369 | |
import_single_Vispa2Matrix | 0.770 | 0.077 | 0.822 | |
inspect_tags | 0.013 | 0.000 | 0.013 | |
integration_alluvial_plot | 2.697 | 0.097 | 8.121 | |
is_sharing | 0.715 | 0.053 | 6.839 | |
iss_source | 0.819 | 0.072 | 6.191 | |
known_clinical_oncogenes | 0.007 | 0.004 | 0.011 | |
mandatory_IS_vars | 0.078 | 0.020 | 0.098 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.143 | 0.012 | 0.154 | |
outliers_by_pool_fragments | 0.137 | 0.004 | 0.141 | |
pcr_id_column | 0.018 | 0.000 | 0.018 | |
purity_filter | 0.302 | 0.024 | 0.326 | |
quantification_types | 0 | 0 | 0 | |
realign_after_collisions | 0.610 | 0.080 | 5.208 | |
reduced_AF_columns | 0.040 | 0.004 | 0.044 | |
refGene_table_cols | 0.001 | 0.000 | 0.000 | |
remove_collisions | 0.641 | 0.067 | 5.318 | |
reset_mandatory_IS_vars | 0.005 | 0.000 | 0.005 | |
sample_statistics | 0.295 | 0.052 | 0.347 | |
separate_quant_matrices | 0.016 | 0.000 | 0.016 | |
set_mandatory_IS_vars | 0.097 | 0.007 | 0.104 | |
set_matrix_file_suffixes | 0.014 | 0.004 | 0.019 | |
sharing_heatmap | 1.181 | 0.123 | 8.344 | |
sharing_venn | 2.121 | 0.217 | 29.565 | |
threshold_filter | 0.001 | 0.001 | 0.000 | |
top_abund_tableGrob | 0.615 | 0.047 | 0.662 | |
top_cis_overtime_heatmap | 1.194 | 0.121 | 6.238 | |
top_integrations | 0.029 | 0.000 | 0.029 | |
top_targeted_genes | 0.440 | 0.016 | 0.456 | |
transform_columns | 0.013 | 0.008 | 0.020 | |