Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-21 11:36:09 -0400 (Tue, 21 May 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" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4515 |
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 | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 2024-05-20 23:36:11 -0400 (Mon, 20 May 2024) |
EndedAt: 2024-05-20 23:45:30 -0400 (Mon, 20 May 2024) |
EllapsedTime: 559.2 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 2.823 0.087 8.048 sharing_venn 2.372 0.229 28.561 import_parallel_Vispa2Matrices 1.753 0.213 11.943 sharing_heatmap 1.262 0.131 8.356 import_Vispa2_stats 1.203 0.179 5.747 CIS_grubbs_overtime 1.268 0.078 6.217 top_cis_overtime_heatmap 1.172 0.141 6.121 iss_source 0.767 0.089 6.142 is_sharing 0.772 0.046 6.979 HSC_population_plot 0.768 0.009 5.524 compute_near_integrations 0.701 0.019 8.711 remove_collisions 0.642 0.043 5.173 HSC_population_size_estimate 0.471 0.002 5.220 * 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/RtmppKJkLY/file2f4df57e0e4313/2024-05-20_collision_removal_report.html Report correctly saved i Report saved to: /tmp/RtmppKJkLY/file2f4df55c661dc3/2024-05-20_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ] > > proc.time() user system elapsed 85.610 5.666 239.693
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 0.916 | 0.103 | 1.020 | |
CIS_grubbs_overtime | 1.268 | 0.078 | 6.217 | |
CIS_volcano_plot | 1.194 | 0.048 | 1.241 | |
HSC_population_plot | 0.768 | 0.009 | 5.524 | |
HSC_population_size_estimate | 0.471 | 0.002 | 5.220 | |
NGSdataExplorer | 0.001 | 0.000 | 0.000 | |
aggregate_metadata | 0.097 | 0.000 | 0.097 | |
aggregate_values_by_key | 0.07 | 0.00 | 0.07 | |
annotation_issues | 0.026 | 0.000 | 0.027 | |
as_sparse_matrix | 0.048 | 0.000 | 0.048 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0.021 | 0.000 | 0.021 | |
blood_lineages_default | 0.017 | 0.004 | 0.020 | |
circos_genomic_density | 0.000 | 0.000 | 0.001 | |
clinical_relevant_suspicious_genes | 0.012 | 0.000 | 0.012 | |
comparison_matrix | 0.032 | 0.000 | 0.033 | |
compute_abundance | 0.036 | 0.000 | 0.035 | |
compute_near_integrations | 0.701 | 0.019 | 8.711 | |
cumulative_count_union | 0.001 | 0.000 | 0.001 | |
cumulative_is | 0.171 | 0.008 | 0.179 | |
date_formats | 0 | 0 | 0 | |
default_af_transform | 0 | 0 | 0 | |
default_iss_file_prefixes | 0 | 0 | 0 | |
default_meta_agg | 0.013 | 0.003 | 0.016 | |
default_rec_agg_lambdas | 0 | 0 | 0 | |
default_report_path | 0.007 | 0.000 | 0.007 | |
default_stats | 1.021 | 0.064 | 1.085 | |
enable_progress_bars | 0.008 | 0.008 | 0.017 | |
export_ISA_settings | 0.068 | 0.000 | 0.068 | |
fisher_scatterplot | 1.277 | 0.044 | 1.321 | |
gene_frequency_fisher | 0.782 | 0.036 | 0.818 | |
generate_Vispa2_launch_AF | 0.174 | 0.005 | 0.199 | |
generate_blank_association_file | 0.013 | 0.000 | 0.013 | |
generate_default_folder_structure | 0.394 | 0.053 | 0.420 | |
import_ISA_settings | 0.062 | 0.003 | 0.066 | |
import_Vispa2_stats | 1.203 | 0.179 | 5.747 | |
import_association_file | 0.545 | 0.132 | 0.643 | |
import_parallel_Vispa2Matrices | 1.753 | 0.213 | 11.943 | |
import_single_Vispa2Matrix | 0.767 | 0.155 | 0.896 | |
inspect_tags | 0.009 | 0.004 | 0.013 | |
integration_alluvial_plot | 2.823 | 0.087 | 8.048 | |
is_sharing | 0.772 | 0.046 | 6.979 | |
iss_source | 0.767 | 0.089 | 6.142 | |
known_clinical_oncogenes | 0.014 | 0.000 | 0.013 | |
mandatory_IS_vars | 0.093 | 0.008 | 0.101 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.131 | 0.040 | 0.171 | |
outliers_by_pool_fragments | 0.149 | 0.000 | 0.149 | |
pcr_id_column | 0.019 | 0.000 | 0.020 | |
purity_filter | 0.321 | 0.032 | 0.353 | |
quantification_types | 0.001 | 0.000 | 0.000 | |
realign_after_collisions | 0.748 | 0.043 | 4.896 | |
reduced_AF_columns | 0.046 | 0.000 | 0.045 | |
refGene_table_cols | 0.001 | 0.000 | 0.000 | |
remove_collisions | 0.642 | 0.043 | 5.173 | |
reset_mandatory_IS_vars | 0.004 | 0.004 | 0.007 | |
sample_statistics | 0.308 | 0.072 | 0.380 | |
separate_quant_matrices | 0.016 | 0.000 | 0.017 | |
set_mandatory_IS_vars | 0.090 | 0.016 | 0.107 | |
set_matrix_file_suffixes | 0.018 | 0.000 | 0.018 | |
sharing_heatmap | 1.262 | 0.131 | 8.356 | |
sharing_venn | 2.372 | 0.229 | 28.561 | |
threshold_filter | 0.000 | 0.000 | 0.001 | |
top_abund_tableGrob | 0.579 | 0.052 | 0.632 | |
top_cis_overtime_heatmap | 1.172 | 0.141 | 6.121 | |
top_integrations | 0.03 | 0.00 | 0.03 | |
top_targeted_genes | 0.445 | 0.015 | 0.460 | |
transform_columns | 0.014 | 0.004 | 0.018 | |