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This page was generated on 2024-05-04 11:36:43 -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 nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ISAnalytics_1.14.0.tar.gz
StartedAt: 2024-05-04 00:22:40 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 00:32:04 -0400 (Sat, 04 May 2024)
EllapsedTime: 564.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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      2.782  0.110   8.304
sharing_venn                   2.473  0.229  28.473
import_parallel_Vispa2Matrices 1.936  0.231  13.008
CIS_grubbs_overtime            1.561  0.104   6.699
import_Vispa2_stats            1.295  0.156   6.103
top_cis_overtime_heatmap       1.238  0.136   6.359
sharing_heatmap                1.231  0.093   7.873
iss_source                     0.815  0.072   6.115
HSC_population_plot            0.826  0.046   5.827
is_sharing                     0.688  0.041   6.280
remove_collisions              0.678  0.039   5.199
realign_after_collisions       0.687  0.025   5.166
compute_near_integrations      0.657  0.013   9.213
HSC_population_size_estimate   0.529  0.013   5.247
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.19-bioc/R/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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)

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: x86_64-pc-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: /tmp/RtmpIJ8gHG/filecc8de28c3b5c5/2024-05-04_collision_removal_report.html
Report correctly saved
i Report saved to: /tmp/RtmpIJ8gHG/filecc8de8fba7cb/2024-05-04_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
 84.454   5.813 239.335 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.0070.0801.086
CIS_grubbs_overtime1.5610.1046.699
CIS_volcano_plot1.2790.0601.340
HSC_population_plot0.8260.0465.827
HSC_population_size_estimate0.5290.0135.247
NGSdataExplorer000
aggregate_metadata0.1350.0000.135
aggregate_values_by_key0.0780.0000.078
annotation_issues0.0320.0000.032
as_sparse_matrix0.0660.0120.078
available_outlier_tests000
available_tags0.0210.0120.033
blood_lineages_default0.0280.0000.028
circos_genomic_density0.0000.0000.001
clinical_relevant_suspicious_genes0.0170.0000.017
comparison_matrix0.0370.0190.056
compute_abundance0.0360.0080.043
compute_near_integrations0.6570.0139.213
cumulative_count_union000
cumulative_is0.1500.0070.156
date_formats0.0010.0000.000
default_af_transform0.0010.0000.001
default_iss_file_prefixes0.0010.0000.000
default_meta_agg0.0150.0000.015
default_rec_agg_lambdas0.0000.0000.001
default_report_path0.0040.0030.007
default_stats1.0670.0721.139
enable_progress_bars0.0140.0010.015
export_ISA_settings0.0660.0020.068
fisher_scatterplot1.3670.0761.443
gene_frequency_fisher0.9010.0080.909
generate_Vispa2_launch_AF0.1950.0140.227
generate_blank_association_file0.0150.0000.015
generate_default_folder_structure0.4090.0600.443
import_ISA_settings0.0650.0000.066
import_Vispa2_stats1.2950.1566.103
import_association_file0.5940.1270.685
import_parallel_Vispa2Matrices 1.936 0.23113.008
import_single_Vispa2Matrix1.0670.4051.447
inspect_tags0.0130.0000.013
integration_alluvial_plot2.7820.1108.304
is_sharing0.6880.0416.280
iss_source0.8150.0726.115
known_clinical_oncogenes0.0040.0080.011
mandatory_IS_vars0.0930.0080.101
matching_options000
outlier_filter0.1450.0190.165
outliers_by_pool_fragments0.1450.0000.145
pcr_id_column0.0190.0000.019
purity_filter0.3100.0280.338
quantification_types0.0010.0000.000
realign_after_collisions0.6870.0255.166
reduced_AF_columns0.0470.0080.054
refGene_table_cols0.0010.0000.000
remove_collisions0.6780.0395.199
reset_mandatory_IS_vars0.0050.0000.005
sample_statistics0.2860.0520.338
separate_quant_matrices0.0100.0080.018
set_mandatory_IS_vars0.1060.0040.110
set_matrix_file_suffixes0.0170.0000.018
sharing_heatmap1.2310.0937.873
sharing_venn 2.473 0.22928.473
threshold_filter000
top_abund_tableGrob0.6360.0400.676
top_cis_overtime_heatmap1.2380.1366.359
top_integrations0.0300.0040.033
top_targeted_genes0.4810.0200.501
transform_columns0.0160.0040.020