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This page was generated on 2024-05-04 11:40:40 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1061/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.14.0  (landing page)
Giulia Pais
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: RELEASE_3_19
git_last_commit: 5effb43
git_last_commit_date: 2024-04-30 11:26:39 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ISAnalytics on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ISAnalytics
Version: 1.14.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ISAnalytics_1.14.0.tar.gz
StartedAt: 2024-05-04 08:44:07 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 08:53:52 -0000 (Sat, 04 May 2024)
EllapsedTime: 585.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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      4.368  0.174  11.339
sharing_venn                   3.219  0.440  42.571
import_parallel_Vispa2Matrices 2.238  0.209  15.657
sharing_heatmap                1.674  0.138  11.507
CIS_grubbs_overtime            1.645  0.110   8.140
top_cis_overtime_heatmap       1.562  0.189   8.259
import_Vispa2_stats            1.503  0.165   7.447
iss_source                     1.029  0.036   7.959
compute_near_integrations      0.616  0.389  11.849
HSC_population_plot            0.926  0.048   7.167
is_sharing                     0.868  0.084   9.488
remove_collisions              0.889  0.039   6.919
realign_after_collisions       0.823  0.053   6.660
HSC_population_size_estimate   0.629  0.021   6.933
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.


Installation output

ISAnalytics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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)

Tests output

ISAnalytics.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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: /home/biocbuild/tmp/RtmpJ71ibp/file11f52667e63138/2024-05-04_collision_removal_report.html
Report correctly saved
i Report saved to: /home/biocbuild/tmp/RtmpJ71ibp/file11f5263ee84cd6/2024-05-04_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
122.776   6.790 322.662 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.3820.0511.439
CIS_grubbs_overtime1.6450.1108.140
CIS_volcano_plot1.7950.0201.818
HSC_population_plot0.9260.0487.167
HSC_population_size_estimate0.6290.0216.933
NGSdataExplorer000
aggregate_metadata0.1590.0000.159
aggregate_values_by_key0.1120.0000.112
annotation_issues0.0410.0000.041
as_sparse_matrix0.0790.0000.080
available_outlier_tests0.0000.0000.001
available_tags0.0360.0000.037
blood_lineages_default0.0370.0000.037
circos_genomic_density0.0010.0000.000
clinical_relevant_suspicious_genes0.020.000.02
comparison_matrix0.0590.0000.059
compute_abundance0.0530.0000.053
compute_near_integrations 0.616 0.38911.849
cumulative_count_union0.0000.0000.001
cumulative_is0.2510.0040.256
date_formats000
default_af_transform000
default_iss_file_prefixes000
default_meta_agg0.0250.0000.025
default_rec_agg_lambdas000
default_report_path0.010.000.01
default_stats1.3490.1041.455
enable_progress_bars0.0170.0040.021
export_ISA_settings0.1060.0000.106
fisher_scatterplot1.8170.0511.873
gene_frequency_fisher1.2610.0361.300
generate_Vispa2_launch_AF0.2750.0060.278
generate_blank_association_file0.0170.0000.018
generate_default_folder_structure0.5350.0930.587
import_ISA_settings0.0920.0000.092
import_Vispa2_stats1.5030.1657.447
import_association_file0.8450.1710.965
import_parallel_Vispa2Matrices 2.238 0.20915.657
import_single_Vispa2Matrix1.1530.1731.284
inspect_tags0.0190.0000.019
integration_alluvial_plot 4.368 0.17411.339
is_sharing0.8680.0849.488
iss_source1.0290.0367.959
known_clinical_oncogenes0.0090.0080.016
mandatory_IS_vars0.1480.0080.156
matching_options000
outlier_filter0.1990.0440.244
outliers_by_pool_fragments0.2130.0120.226
pcr_id_column0.0220.0040.027
purity_filter0.4940.0280.524
quantification_types0.0000.0000.001
realign_after_collisions0.8230.0536.660
reduced_AF_columns0.0650.0160.080
refGene_table_cols0.0010.0000.001
remove_collisions0.8890.0396.919
reset_mandatory_IS_vars0.0070.0000.007
sample_statistics0.4790.0150.495
separate_quant_matrices0.0160.0040.020
set_mandatory_IS_vars0.1340.0150.149
set_matrix_file_suffixes0.0260.0000.027
sharing_heatmap 1.674 0.13811.507
sharing_venn 3.219 0.44042.571
threshold_filter0.0010.0000.000
top_abund_tableGrob1.0670.1161.185
top_cis_overtime_heatmap1.5620.1898.259
top_integrations0.0250.0320.057
top_targeted_genes0.6560.0840.742
transform_columns0.0280.0000.029