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This page was generated on 2024-05-04 11:39:24 -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 lconway


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.

raw results


Summary

Package: ISAnalytics
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ISAnalytics_1.14.0.tar.gz
StartedAt: 2024-05-03 22:42:08 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:51:28 -0400 (Fri, 03 May 2024)
EllapsedTime: 559.5 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ISAnalytics_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 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      3.272  0.074  10.065
import_parallel_Vispa2Matrices 1.861  0.152  14.580
CIS_grubbs_overtime            1.553  0.243   8.429
import_Vispa2_stats            1.326  0.137   7.055
sharing_venn                   1.360  0.092  40.051
top_cis_overtime_heatmap       1.272  0.051   7.670
sharing_heatmap                1.259  0.034  10.454
iss_source                     0.808  0.026   7.422
HSC_population_plot            0.750  0.022   6.260
remove_collisions              0.739  0.027   6.531
is_sharing                     0.721  0.027   8.418
realign_after_collisions       0.683  0.024   6.398
compute_near_integrations      0.600  0.023  10.982
HSC_population_size_estimate   0.547  0.017   6.682
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.


Installation output

ISAnalytics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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
2024-05-03 22:47:21.885 R[85676:1725336868] XType: com.apple.fonts is not accessible.
2024-05-03 22:47:21.886 R[85676:1725336868] XType: XTFontStaticRegistry is enabled.
Report correctly saved
i Report saved to: /tmp/RtmpWzGPcr/file14eac2ff4473e/2024-05-03_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpWzGPcr/file14eac592513fe/2024-05-03_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
102.804   5.856 299.604 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.1730.0641.247
CIS_grubbs_overtime1.5530.2438.429
CIS_volcano_plot1.4900.0341.535
HSC_population_plot0.7500.0226.260
HSC_population_size_estimate0.5470.0176.682
NGSdataExplorer0.0000.0000.001
aggregate_metadata0.1220.0020.126
aggregate_values_by_key0.0880.0040.093
annotation_issues0.0300.0020.032
as_sparse_matrix0.0670.0030.070
available_outlier_tests0.0010.0000.001
available_tags0.030.000.03
blood_lineages_default0.0290.0000.030
circos_genomic_density000
clinical_relevant_suspicious_genes0.0190.0010.019
comparison_matrix0.0460.0010.048
compute_abundance0.0450.0020.048
compute_near_integrations 0.600 0.02310.982
cumulative_count_union000
cumulative_is0.1920.0040.199
date_formats0.0010.0010.000
default_af_transform0.0010.0000.001
default_iss_file_prefixes000
default_meta_agg0.0180.0000.018
default_rec_agg_lambdas0.0010.0000.000
default_report_path0.0100.0010.011
default_stats1.2140.0501.273
enable_progress_bars0.0190.0040.023
export_ISA_settings0.0940.0080.104
fisher_scatterplot1.2370.0381.282
gene_frequency_fisher1.3760.0241.409
generate_Vispa2_launch_AF0.2530.0230.286
generate_blank_association_file0.0140.0010.016
generate_default_folder_structure0.4760.0900.515
import_ISA_settings0.0720.0020.074
import_Vispa2_stats1.3260.1377.055
import_association_file0.7260.1180.779
import_parallel_Vispa2Matrices 1.861 0.15214.580
import_single_Vispa2Matrix1.0070.1331.098
inspect_tags0.0180.0000.019
integration_alluvial_plot 3.272 0.07410.065
is_sharing0.7210.0278.418
iss_source0.8080.0267.422
known_clinical_oncogenes0.0110.0000.011
mandatory_IS_vars0.1190.0100.130
matching_options000
outlier_filter0.2050.0150.221
outliers_by_pool_fragments0.1680.0040.172
pcr_id_column0.0270.0010.028
purity_filter0.4080.0090.420
quantification_types0.0010.0000.000
realign_after_collisions0.6830.0246.398
reduced_AF_columns0.0630.0010.063
refGene_table_cols0.0000.0010.001
remove_collisions0.7390.0276.531
reset_mandatory_IS_vars0.0060.0010.008
sample_statistics0.3960.0620.467
separate_quant_matrices0.0160.0010.016
set_mandatory_IS_vars0.1350.0050.139
set_matrix_file_suffixes0.0260.0010.027
sharing_heatmap 1.259 0.03410.454
sharing_venn 1.360 0.09240.051
threshold_filter0.0000.0010.000
top_abund_tableGrob0.8150.0160.844
top_cis_overtime_heatmap1.2720.0517.670
top_integrations0.0240.0010.025
top_targeted_genes0.4550.0030.459
transform_columns0.0220.0000.023