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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1044/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.17.1  (landing page)
Francesco Gazzo
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: devel
git_last_commit: 3b0f63a
git_last_commit_date: 2024-12-05 05:16:21 -0500 (Thu, 05 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


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: 1.17.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ISAnalytics_1.17.1.tar.gz
StartedAt: 2024-12-24 07:54:30 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 08:04:16 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 585.6 seconds
RetCode: 0
Status:   OK  
CheckDir: ISAnalytics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ISAnalytics_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ISAnalytics.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* this is package ‘ISAnalytics’ version ‘1.17.1’
* 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 ...Warning: program compiled against libxml 212 using older 211
 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      4.167  0.156  11.421
sharing_venn                   3.331  0.299  42.861
import_parallel_Vispa2Matrices 2.250  0.233  15.338
CIS_grubbs_overtime            1.817  0.173   8.578
sharing_heatmap                1.629  0.188  11.680
import_Vispa2_stats            1.491  0.151   7.464
top_cis_overtime_heatmap       1.577  0.036   8.512
iss_source                     1.102  0.030   8.339
HSC_population_plot            0.954  0.115   7.196
is_sharing                     0.908  0.018   9.022
remove_collisions              0.875  0.014   6.868
realign_after_collisions       0.841  0.011   6.672
compute_near_integrations      0.662  0.068  11.619
HSC_population_size_estimate   0.664  0.041   6.975
* 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-3.21-bioc/meat/ISAnalytics.Rcheck/00check.log’
for details.


Installation output

ISAnalytics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL ISAnalytics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
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/RtmpghNxcH/file145f925d9033da/2024-12-24_collision_removal_report.html
Report correctly saved
i Report saved to: /home/biocbuild/tmp/RtmpghNxcH/file145f9220572d87/2024-12-24_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 834 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 834 ]
> 
> proc.time()
   user  system elapsed 
124.738   6.599 323.488 

Example timings

ISAnalytics.Rcheck/ISAnalytics-Ex.timings

nameusersystemelapsed
CIS_grubbs1.3450.0441.392
CIS_grubbs_overtime1.8170.1738.578
CIS_volcano_plot1.8330.1161.955
HSC_population_plot0.9540.1157.196
HSC_population_size_estimate0.6640.0416.975
NGSdataExplorer0.0000.0000.001
aggregate_metadata0.1710.0080.179
aggregate_values_by_key0.0890.0040.093
annotation_issues0.0360.0000.037
as_sparse_matrix0.0730.0000.074
available_outlier_tests000
available_tags0.0310.0000.031
blood_lineages_default0.0380.0000.038
circos_genomic_density000
clinical_relevant_suspicious_genes0.0160.0000.016
comparison_matrix0.0370.0000.037
compute_abundance0.0380.0080.046
compute_near_integrations 0.662 0.06811.619
cumulative_count_union000
cumulative_is0.2170.0160.233
date_formats0.0010.0000.000
default_af_transform0.0010.0000.001
default_iss_file_prefixes000
default_meta_agg0.0230.0000.023
default_rec_agg_lambdas0.0090.0000.009
default_report_path0.010.000.01
default_stats1.3830.0481.434
enable_progress_bars0.020.000.02
export_ISA_settings0.0960.0000.097
fisher_scatterplot1.4960.0561.556
gene_frequency_fisher1.6640.0281.696
generate_Vispa2_launch_AF0.2820.0080.289
generate_blank_association_file0.0170.0000.018
generate_default_folder_structure0.4890.0740.565
import_ISA_settings0.0860.0040.091
import_Vispa2_stats1.4910.1517.464
import_association_file0.7900.1230.917
import_parallel_Vispa2Matrices 2.250 0.23315.338
import_single_Vispa2Matrix1.0750.2091.286
inspect_tags0.0180.0000.018
integration_alluvial_plot 4.167 0.15611.421
is_sharing0.9080.0189.022
iss_source1.1020.0308.339
known_clinical_oncogenes0.0170.0000.017
mandatory_IS_vars0.1260.0200.146
matching_options000
outlier_filter0.2150.0080.223
outliers_by_pool_fragments0.2220.0000.222
pcr_id_column0.0260.0000.025
purity_filter0.4970.0000.499
quantification_types000
realign_after_collisions0.8410.0116.672
reduced_AF_columns0.0620.0000.062
refGene_table_cols000
remove_collisions0.8750.0146.868
reset_mandatory_IS_vars0.0040.0030.007
sample_statistics0.4370.0400.479
separate_quant_matrices0.0150.0040.019
set_mandatory_IS_vars0.1270.0080.135
set_matrix_file_suffixes0.0240.0000.023
sharing_heatmap 1.629 0.18811.680
sharing_venn 3.331 0.29942.861
threshold_filter000
top_abund_tableGrob0.9510.0280.981
top_cis_overtime_heatmap1.5770.0368.512
top_integrations0.0390.0000.038
top_targeted_genes0.7090.0000.714
transform_columns0.0270.0000.028