Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:35 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 982/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISAnalytics 1.9.1 (landing page) Andrea Calabria
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: ISAnalytics |
Version: 1.9.1 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ISAnalytics_1.9.1.tar.gz |
StartedAt: 2022-12-29 00:45:18 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 00:53:12 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 473.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ISAnalytics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ISAnalytics_1.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ISAnalytics.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ISAnalytics/DESCRIPTION' ... OK * this is package 'ISAnalytics' version '1.9.1' * 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 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 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 ... NOTE .sh_row_permut: no visible global function definition for '.' .sharing_multdf_mult_key: no visible binding for global variable '.' .sharing_multdf_single_key: no visible binding for global variable '.' .sharing_singledf_mult_key: no visible binding for global variable '.' .sharing_singledf_single_key: no visible binding for global variable '.' cumulative_is: no visible binding for global variable 'is' gene_frequency_fisher: no visible binding for global variable '.' Undefined global functions or variables: . is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 sharing_venn 28.44 1.07 29.59 import_Vispa2_stats 1.85 0.33 5.88 integration_alluvial_plot 2.12 0.00 7.26 import_parallel_Vispa2Matrices 1.51 0.35 12.01 top_cis_overtime_heatmap 1.55 0.06 6.32 CIS_grubbs_overtime 0.83 0.14 5.89 HSC_population_plot 0.75 0.05 5.15 iss_source 0.69 0.00 5.51 compute_near_integrations 0.22 0.00 7.75 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ISAnalytics.Rcheck/00check.log' for details.
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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) Loading required package: magrittr Attaching package: 'magrittr' The following objects are masked from 'package:testthat': equals, is_less_than, not > > test_check("ISAnalytics") Loading required namespace: plotly Loading required namespace: rmarkdown Report correctly saved i Report saved to: F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/RtmpILfAPj/file2fcc69112de5/2022-12-29_collision_removal_report.html Report correctly saved i Report saved to: F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/RtmpILfAPj/file2fcc37bbae/2022-12-29_outlier_test_pool_fragments_report.html [ FAIL 0 | WARN 31 | SKIP 0 | PASS 836 ] [ FAIL 0 | WARN 31 | SKIP 0 | PASS 836 ] > > proc.time() user system elapsed 77.93 6.45 281.89
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
name | user | system | elapsed | |
CIS_grubbs | 0.62 | 0.07 | 0.74 | |
CIS_grubbs_overtime | 0.83 | 0.14 | 5.89 | |
CIS_volcano_plot | 1.04 | 0.01 | 1.06 | |
HSC_population_plot | 0.75 | 0.05 | 5.15 | |
HSC_population_size_estimate | 0.43 | 0.00 | 4.65 | |
NGSdataExplorer | 0 | 0 | 0 | |
aggregate_metadata | 0.12 | 0.00 | 0.13 | |
aggregate_values_by_key | 0.08 | 0.00 | 0.07 | |
annotation_issues | 0.05 | 0.00 | 0.05 | |
as_sparse_matrix | 0.07 | 0.02 | 0.10 | |
available_outlier_tests | 0 | 0 | 0 | |
available_tags | 0 | 0 | 0 | |
blood_lineages_default | 0.02 | 0.00 | 0.01 | |
circos_genomic_density | 0 | 0 | 0 | |
clinical_relevant_suspicious_genes | 0 | 0 | 0 | |
comparison_matrix | 0.03 | 0.02 | 0.04 | |
compute_abundance | 0.03 | 0.00 | 0.03 | |
compute_near_integrations | 0.22 | 0.00 | 7.75 | |
cumulative_count_union | 0.16 | 0.03 | 0.19 | |
cumulative_is | 0.08 | 0.01 | 0.10 | |
date_formats | 0 | 0 | 0 | |
default_af_transform | 0 | 0 | 0 | |
default_iss_file_prefixes | 0 | 0 | 0 | |
default_meta_agg | 0.01 | 0.00 | 0.02 | |
default_rec_agg_lambdas | 0 | 0 | 0 | |
default_report_path | 0.00 | 0.02 | 0.01 | |
default_stats | 0 | 0 | 0 | |
enable_progress_bars | 0.05 | 0.00 | 0.05 | |
export_ISA_settings | 0.12 | 0.00 | 0.12 | |
fisher_scatterplot | 1.17 | 0.01 | 1.19 | |
gene_frequency_fisher | 1.06 | 0.00 | 1.07 | |
generate_Vispa2_launch_AF | 0.20 | 0.02 | 0.21 | |
generate_blank_association_file | 0 | 0 | 0 | |
generate_default_folder_structure | 0.88 | 0.28 | 0.89 | |
import_ISA_settings | 0.15 | 0.03 | 0.19 | |
import_Vispa2_stats | 1.85 | 0.33 | 5.88 | |
import_association_file | 1.11 | 0.25 | 1.19 | |
import_parallel_Vispa2Matrices | 1.51 | 0.35 | 12.01 | |
import_single_Vispa2Matrix | 1.36 | 0.20 | 1.50 | |
inspect_tags | 0.02 | 0.00 | 0.02 | |
integration_alluvial_plot | 2.12 | 0.00 | 7.26 | |
is_sharing | 1.05 | 0.08 | 1.13 | |
iss_source | 0.69 | 0.00 | 5.51 | |
known_clinical_oncogenes | 0.01 | 0.00 | 0.02 | |
mandatory_IS_vars | 0.08 | 0.00 | 0.08 | |
matching_options | 0 | 0 | 0 | |
outlier_filter | 0.11 | 0.02 | 0.13 | |
outliers_by_pool_fragments | 0.08 | 0.01 | 0.09 | |
pcr_id_column | 0.04 | 0.00 | 0.05 | |
purity_filter | 0.54 | 0.02 | 0.55 | |
quantification_types | 0 | 0 | 0 | |
realign_after_collisions | 0.60 | 0.05 | 4.59 | |
reduced_AF_columns | 0.10 | 0.00 | 0.09 | |
refGene_table_cols | 0 | 0 | 0 | |
remove_collisions | 0.50 | 0.04 | 4.55 | |
reset_mandatory_IS_vars | 0.00 | 0.08 | 0.08 | |
sample_statistics | 1.36 | 0.22 | 1.58 | |
separate_quant_matrices | 0.01 | 0.00 | 0.01 | |
set_mandatory_IS_vars | 0.10 | 0.05 | 0.14 | |
set_matrix_file_suffixes | 0.04 | 0.00 | 0.05 | |
sharing_heatmap | 2.16 | 0.11 | 2.27 | |
sharing_venn | 28.44 | 1.07 | 29.59 | |
threshold_filter | 0.06 | 0.00 | 0.06 | |
top_abund_tableGrob | 0.45 | 0.04 | 0.49 | |
top_cis_overtime_heatmap | 1.55 | 0.06 | 6.32 | |
top_integrations | 0.03 | 0.00 | 0.04 | |
top_targeted_genes | 0.33 | 0.00 | 0.32 | |
transform_columns | 0.00 | 0.01 | 0.02 | |