| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:36 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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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 1008/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ISAnalytics 1.11.1 (landing page) Giulia Pais
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: ISAnalytics |
| Version: 1.11.1 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ISAnalytics_1.11.1.tar.gz |
| StartedAt: 2023-05-30 10:26:25 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 10:38:40 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 735.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ISAnalytics.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings ISAnalytics_1.11.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-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 ‘1.11.1’
* 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 4.037 0.183 11.080
sharing_venn 3.320 0.249 46.259
import_parallel_Vispa2Matrices 2.436 0.217 15.348
CIS_grubbs_overtime 1.619 0.243 8.369
import_Vispa2_stats 1.659 0.134 7.356
top_cis_overtime_heatmap 1.573 0.064 8.036
sharing_heatmap 1.536 0.011 11.092
iss_source 1.124 0.018 7.974
HSC_population_plot 0.992 0.082 7.280
remove_collisions 0.812 0.228 6.773
is_sharing 0.940 0.074 9.094
realign_after_collisions 0.867 0.110 6.703
compute_near_integrations 0.672 0.072 11.151
HSC_population_size_estimate 0.625 0.028 6.805
* 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/R/R-4.3.0/bin/R CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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/RtmpKqOfFP/file1ed4aa24b470f8/2023-05-30_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpKqOfFP/file1ed4aa50f2bfcb/2023-05-30_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 833 ]
>
> proc.time()
user system elapsed
121.823 4.995 314.543
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
| name | user | system | elapsed | |
| CIS_grubbs | 1.225 | 0.069 | 1.293 | |
| CIS_grubbs_overtime | 1.619 | 0.243 | 8.369 | |
| CIS_volcano_plot | 1.657 | 0.064 | 1.721 | |
| HSC_population_plot | 0.992 | 0.082 | 7.280 | |
| HSC_population_size_estimate | 0.625 | 0.028 | 6.805 | |
| NGSdataExplorer | 0 | 0 | 0 | |
| aggregate_metadata | 0.155 | 0.000 | 0.155 | |
| aggregate_values_by_key | 0.113 | 0.064 | 0.177 | |
| annotation_issues | 0.041 | 0.020 | 0.062 | |
| as_sparse_matrix | 0.112 | 0.072 | 0.183 | |
| available_outlier_tests | 0 | 0 | 0 | |
| available_tags | 0.032 | 0.012 | 0.043 | |
| blood_lineages_default | 0.040 | 0.004 | 0.044 | |
| circos_genomic_density | 0 | 0 | 0 | |
| clinical_relevant_suspicious_genes | 0.010 | 0.008 | 0.018 | |
| comparison_matrix | 0.040 | 0.004 | 0.044 | |
| compute_abundance | 0.055 | 0.000 | 0.055 | |
| compute_near_integrations | 0.672 | 0.072 | 11.151 | |
| cumulative_count_union | 0.000 | 0.000 | 0.001 | |
| cumulative_is | 0.253 | 0.130 | 0.384 | |
| date_formats | 0.000 | 0.000 | 0.001 | |
| default_af_transform | 0.001 | 0.000 | 0.001 | |
| default_iss_file_prefixes | 0 | 0 | 0 | |
| default_meta_agg | 0.031 | 0.000 | 0.031 | |
| default_rec_agg_lambdas | 0.000 | 0.000 | 0.001 | |
| default_report_path | 0.011 | 0.002 | 0.013 | |
| default_stats | 1.392 | 0.056 | 1.448 | |
| enable_progress_bars | 0.024 | 0.000 | 0.024 | |
| export_ISA_settings | 0.422 | 0.004 | 0.425 | |
| fisher_scatterplot | 1.454 | 0.156 | 1.610 | |
| gene_frequency_fisher | 1.267 | 0.064 | 1.332 | |
| generate_Vispa2_launch_AF | 0.272 | 0.002 | 0.271 | |
| generate_blank_association_file | 0.017 | 0.000 | 0.017 | |
| generate_default_folder_structure | 0.614 | 0.143 | 0.713 | |
| import_ISA_settings | 0.098 | 0.003 | 0.103 | |
| import_Vispa2_stats | 1.659 | 0.134 | 7.356 | |
| import_association_file | 0.907 | 0.163 | 1.016 | |
| import_parallel_Vispa2Matrices | 2.436 | 0.217 | 15.348 | |
| import_single_Vispa2Matrix | 1.183 | 0.225 | 1.364 | |
| inspect_tags | 0.021 | 0.000 | 0.021 | |
| integration_alluvial_plot | 4.037 | 0.183 | 11.080 | |
| is_sharing | 0.940 | 0.074 | 9.094 | |
| iss_source | 1.124 | 0.018 | 7.974 | |
| known_clinical_oncogenes | 0.014 | 0.000 | 0.013 | |
| mandatory_IS_vars | 0.123 | 0.000 | 0.122 | |
| matching_options | 0.001 | 0.000 | 0.000 | |
| outlier_filter | 0.222 | 0.004 | 0.227 | |
| outliers_by_pool_fragments | 0.243 | 0.000 | 0.244 | |
| pcr_id_column | 0.034 | 0.000 | 0.035 | |
| purity_filter | 0.551 | 0.004 | 0.555 | |
| quantification_types | 0 | 0 | 0 | |
| realign_after_collisions | 0.867 | 0.110 | 6.703 | |
| reduced_AF_columns | 0.072 | 0.024 | 0.096 | |
| refGene_table_cols | 0.001 | 0.000 | 0.000 | |
| remove_collisions | 0.812 | 0.228 | 6.773 | |
| reset_mandatory_IS_vars | 0.015 | 0.001 | 0.015 | |
| sample_statistics | 0.403 | 0.023 | 0.427 | |
| separate_quant_matrices | 0.021 | 0.001 | 0.022 | |
| set_mandatory_IS_vars | 0.12 | 0.00 | 0.12 | |
| set_matrix_file_suffixes | 0.04 | 0.00 | 0.04 | |
| sharing_heatmap | 1.536 | 0.011 | 11.092 | |
| sharing_venn | 3.320 | 0.249 | 46.259 | |
| threshold_filter | 0.000 | 0.000 | 0.001 | |
| top_abund_tableGrob | 1.031 | 0.027 | 1.059 | |
| top_cis_overtime_heatmap | 1.573 | 0.064 | 8.036 | |
| top_integrations | 0.061 | 0.000 | 0.061 | |
| top_targeted_genes | 1.061 | 0.000 | 1.060 | |
| transform_columns | 0.026 | 0.000 | 0.026 | |