Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:26 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1013/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.9.3 (landing page) Giulia Pais
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: ISAnalytics |
Version: 1.9.3 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ISAnalytics_1.9.3.tar.gz |
StartedAt: 2023-04-11 21:06:16 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 21:16:00 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 583.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ISAnalytics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ISAnalytics_1.9.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ISAnalytics.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘ISAnalytics/DESCRIPTION’ ... OK * this is package ‘ISAnalytics’ version ‘1.9.3’ * 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 R 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 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 ... OK * 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 3.125 0.213 9.247 sharing_venn 2.849 0.236 35.005 import_parallel_Vispa2Matrices 1.953 0.189 12.915 import_Vispa2_stats 1.501 0.146 6.329 CIS_grubbs_overtime 1.338 0.075 6.625 sharing_heatmap 1.253 0.117 9.111 top_cis_overtime_heatmap 1.279 0.089 6.482 iss_source 0.914 0.077 6.321 is_sharing 0.883 0.073 7.581 realign_after_collisions 0.796 0.059 5.608 HSC_population_plot 0.764 0.016 5.875 remove_collisions 0.672 0.080 5.211 HSC_population_size_estimate 0.526 0.016 5.387 compute_near_integrations 0.445 0.008 8.954 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ISAnalytics.Rmd’ using ‘UTF-8’... OK ‘workflow_start.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154) Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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/RtmpO2WZHL/file20dc885c14bd28/2023-04-11_collision_removal_report.html Report correctly saved i Report saved to: /tmp/RtmpO2WZHL/file20dc8835d23ae5/2023-04-11_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 0 | SKIP 0 | PASS 833 ] > > proc.time() user system elapsed 93.757 5.643 252.689
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 0.954 | 0.072 | 1.026 | |
CIS_grubbs_overtime | 1.338 | 0.075 | 6.625 | |
CIS_volcano_plot | 1.229 | 0.028 | 1.257 | |
HSC_population_plot | 0.764 | 0.016 | 5.875 | |
HSC_population_size_estimate | 0.526 | 0.016 | 5.387 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.134 | 0.004 | 0.139 | |
aggregate_values_by_key | 0.114 | 0.000 | 0.114 | |
annotation_issues | 0.047 | 0.000 | 0.046 | |
as_sparse_matrix | 0.065 | 0.004 | 0.069 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0.022 | 0.000 | 0.022 | |
blood_lineages_default | 0.027 | 0.004 | 0.032 | |
circos_genomic_density | 0 | 0 | 0 | |
clinical_relevant_suspicious_genes | 0.012 | 0.000 | 0.013 | |
comparison_matrix | 0.027 | 0.004 | 0.031 | |
compute_abundance | 0.039 | 0.000 | 0.039 | |
compute_near_integrations | 0.445 | 0.008 | 8.954 | |
cumulative_count_union | 0 | 0 | 0 | |
cumulative_is | 0.182 | 0.000 | 0.182 | |
date_formats | 0 | 0 | 0 | |
default_af_transform | 0.000 | 0.000 | 0.001 | |
default_iss_file_prefixes | 0.000 | 0.000 | 0.001 | |
default_meta_agg | 0.017 | 0.000 | 0.017 | |
default_rec_agg_lambdas | 0.000 | 0.000 | 0.001 | |
default_report_path | 0.007 | 0.000 | 0.008 | |
default_stats | 1.164 | 0.072 | 1.236 | |
enable_progress_bars | 0.010 | 0.005 | 0.016 | |
export_ISA_settings | 0.070 | 0.002 | 0.072 | |
fisher_scatterplot | 1.083 | 0.028 | 1.112 | |
gene_frequency_fisher | 0.920 | 0.048 | 0.968 | |
generate_Vispa2_launch_AF | 0.209 | 0.012 | 0.239 | |
generate_blank_association_file | 0.008 | 0.008 | 0.016 | |
generate_default_folder_structure | 0.489 | 0.091 | 0.557 | |
import_ISA_settings | 0.077 | 0.000 | 0.077 | |
import_Vispa2_stats | 1.501 | 0.146 | 6.329 | |
import_association_file | 0.647 | 0.159 | 0.772 | |
import_parallel_Vispa2Matrices | 1.953 | 0.189 | 12.915 | |
import_single_Vispa2Matrix | 1.152 | 0.168 | 1.295 | |
inspect_tags | 0.017 | 0.000 | 0.017 | |
integration_alluvial_plot | 3.125 | 0.213 | 9.247 | |
is_sharing | 0.883 | 0.073 | 7.581 | |
iss_source | 0.914 | 0.077 | 6.321 | |
known_clinical_oncogenes | 0.009 | 0.004 | 0.013 | |
mandatory_IS_vars | 0.091 | 0.008 | 0.099 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.166 | 0.028 | 0.194 | |
outliers_by_pool_fragments | 0.171 | 0.004 | 0.175 | |
pcr_id_column | 0.025 | 0.003 | 0.029 | |
purity_filter | 0.378 | 0.036 | 0.414 | |
quantification_types | 0 | 0 | 0 | |
realign_after_collisions | 0.796 | 0.059 | 5.608 | |
reduced_AF_columns | 0.056 | 0.000 | 0.056 | |
refGene_table_cols | 0.001 | 0.000 | 0.000 | |
remove_collisions | 0.672 | 0.080 | 5.211 | |
reset_mandatory_IS_vars | 0.012 | 0.001 | 0.011 | |
sample_statistics | 0.275 | 0.059 | 0.334 | |
separate_quant_matrices | 0.021 | 0.000 | 0.020 | |
set_mandatory_IS_vars | 0.101 | 0.008 | 0.110 | |
set_matrix_file_suffixes | 0.019 | 0.004 | 0.024 | |
sharing_heatmap | 1.253 | 0.117 | 9.111 | |
sharing_venn | 2.849 | 0.236 | 35.005 | |
threshold_filter | 0 | 0 | 0 | |
top_abund_tableGrob | 0.699 | 0.064 | 0.763 | |
top_cis_overtime_heatmap | 1.279 | 0.089 | 6.482 | |
top_integrations | 0.031 | 0.000 | 0.031 | |
top_targeted_genes | 0.761 | 0.028 | 0.789 | |
transform_columns | 0.019 | 0.000 | 0.020 | |