Multiple platform build/check report for BioC 3.20 - CHECK results for gINTomics on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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*

CHECK results for gINTomics on kunpeng2

To the developers/maintainers of the gINTomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.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: gINTomics

Version: 1.2.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gINTomics_1.2.0.tar.gz

StartedAt: 2024-11-20 08:24:33 -0000 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 09:04:34 -0000 (Wed, 20 Nov 2024)

EllapsedTime: 2400.3 seconds

RetCode: None

Status: TIMEOUT

CheckDir: gINTomics.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gINTomics_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gINTomics.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘gINTomics/DESCRIPTION’ ... OK
* this is package ‘gINTomics’ version ‘1.2.0’
* 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 ‘gINTomics’ 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 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
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:29:14] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:29:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 08:29:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:29:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 08:29:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:29:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 08:29:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:29:15] [TRACE]   [OmnipathR] Cache locked: FALSE
.build_histo: no visible binding for global variable ‘chr_cov’
.build_histo: no visible binding for global variable ‘significance’
.build_ridge: no visible binding for global variable ‘coef’
.build_ridge: no visible binding for global variable ‘significance’
.circos_preprocess: no visible binding for global variable ‘cnv_met’
.prepare_cnv_heatmap: no visible binding for global variable ‘cnv’
.prepare_gen_heatmap: no visible binding for global variable ‘met’
.prepare_gen_heatmap: no visible binding for global variable ‘cnv’
.prepare_met_heatmap: no visible binding for global variable ‘met’
.prepare_mirna_heatmap: no visible binding for global variable
  ‘mirna_cnv’
.prepare_network: no visible binding for global variable ‘omics’
.prepare_reactive_histo_tf: no visible binding for global variable
  ‘Freq’
.prepare_reactive_venn: no visible binding for global variable
  ‘cnv_met’
.prepare_reactive_venn: no visible binding for global variable ‘pval’
.shiny_preprocess: no visible binding for global variable ‘cov’
plot_tf_distribution: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
  Freq chr_cov cnv cnv_met coef cov met mirna_cnv omics pval
  significance
Consider adding
  importFrom("stats", "coef", "cov")
to your NAMESPACE file.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘gINTomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_volcano
> ### Title: plotting volcano
> ### Aliases: plot_volcano
> 
> ### ** Examples
> 
> # Example usage:
> library(MultiAssayExperiment)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

> data("mmultiassay_ov")
> tmp <- lapply(experiments(mmultiassay_ov), function(x) x[1:20,])
> mmultiassay_ov <- MultiAssayExperiment(experiments = tmp)
> multiomics_integration <- run_multiomics(data = mmultiassay_ov)
--------------Running gene genomic integration--------------
Generating interactions
---------------Running miRNA CNV integration----------------
Generating interactions
removing response variables with zero standard deviation
Warning in .data_check(response_var = response_var, covariates = covariates,  :
  No genes left in common between response_var and interactions
-------------------Running TF integration-------------------
Warning in import_tf_target_interactions(organism = org[species]) :
  'import_tf_target_interactions' is deprecated.
Use 'tf_target' instead.
See help("Deprecated")
[2024-11-20 08:32:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2024-11-20 08:32:49] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 08:32:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:32:49] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 08:32:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:32:49] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-11-20 08:32:49] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-11-20 08:32:49] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:32:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:35:51] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 08:35:51] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-11-20 08:35:56] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:38:58] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 08:38:58] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-11-20 08:39:03] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:42:04] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 08:42:04] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
Error in `map_int()`:
ℹ In index: 1.
ℹ With name: hsa.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 404
Backtrace:
     ▆
  1. ├─gINTomics::run_multiomics(data = mmultiassay_ov)
  2. │ └─gINTomics::run_tf_integration(...)
  3. │   └─gINTomics:::.def_tf_integration(...)
  4. │     └─gINTomics:::.download_tf(genes = colnames(expression), species = species)
  5. │       └─OmnipathR::import_tf_target_interactions(organism = org[species])
  6. │         └─OmnipathR::tf_target(...)
  7. │           ├─rlang::exec(omnipath_query, !!!args)
  8. │           └─OmnipathR (local) `<fn>`(organisms = `<dbl>`, query_type = "interactions", datasets = "tf_target")
  9. │             └─environment() %>% as.list %>% c(list(...)) %>% ...
 10. ├─OmnipathR:::omnipath_check_param(.)
 11. │ └─param$organisms %<>% map_int(ncbi_taxid)
 12. ├─purrr::map_int(., ncbi_taxid)
 13. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 14. │   ├─purrr:::with_indexed_errors(...)
 15. │   │ └─base::withCallingHandlers(...)
 16. │   ├─purrr:::call_with_cleanup(...)
 17. │   └─OmnipathR (local) .f(.x[[i]], ...)
 18. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 19. ├─purrr::map_int(., taxon_name, "ncbi")
 20. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 21. │   ├─purrr:::with_indexed_errors(...)
 22. │   │ └─base::withCallingHandlers(...)
 23. │   ├─purrr:::call_with_cleanup(...)
 24. │   └─OmnipathR (local) .f(.x[[i]], ...)
 25. │     ├─... %>% if_null_len0(NA)
 26. │     └─OmnipathR::get_db("organisms")
 27. │       └─OmnipathR::load_db(key, param = param)
 28. │         ├─rlang::exec(loader, !!!param)
 29. │         └─OmnipathR (local) `<fn>`()
 30. │           ├─... %>% ...
 31. │           └─OmnipathR::ensembl_organisms()
 32. │             ├─... %>% ...
 33. │             └─OmnipathR::ensembl_organisms_raw()
 34. │               └─... %>% html_table()
 35. ├─OmnipathR:::if_null_len0(., NA)
 36. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 37. ├─OmnipathR:::is_empty_2(.)
 38. │ └─value %>% ...
 39. ├─dplyr::first(.)
 40. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 41. │   └─vctrs::vec_size(x)
 42. ├─dplyr::pull(., name_type)
 43. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 44. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 45. ├─dplyr::mutate(...)
 46. ├─dplyr::full_join(...)
 47. ├─dplyr::mutate(...)
 48. ├─dplyr::select(...)
 49. ├─rvest::html_table(.)
 50. ├─rvest::html_element(., "table")
 51. ├─xml2::read_html(.)
 52. ├─OmnipathR:::download_to_cache(., req_headers = user_agent())
 53. │ └─OmnipathR:::download_base(...)
 54. │   └─base::stop(result)
 55. └─purrr (local) `<fn>`(`<smplErrr>`)
 56.   └─cli::cli_abort(...)
 57.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

gINTomics.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘gINTomics’ ...
** using staged installation
** R
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:14:46] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:14:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:14:46] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:09] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:15:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:10] [TRACE]   [OmnipathR] Cache locked: FALSE
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:41] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:15:41] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:16:04] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:16:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:16:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:16:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:16:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:16:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:16:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:16:05] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (gINTomics)

Tests output

gINTomics.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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(gINTomics)
[2024-11-20 08:42:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:42:23] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 08:42:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 08:42:23] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 08:42:23] [TRACE]   [OmnipathR] Contains 2 files.
[2024-11-20 08:42:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 08:42:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:42:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:42:24] [TRACE]   [OmnipathR] Cache locked: FALSE



> 
> test_check("gINTomics")
[2024-11-20 08:42:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2024-11-20 08:42:29] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 08:42:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:42:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:42:29] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 08:42:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:42:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:42:29] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-11-20 08:42:29] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-11-20 08:42:29] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:42:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:45:31] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 08:45:31] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-11-20 08:45:36] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:48:38] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 08:48:38] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-11-20 08:48:43] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:51:44] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 08:51:44] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-11-20 08:51:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2024-11-20 08:51:45] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 08:51:45] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 08:51:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 08:51:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 08:51:45] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-11-20 08:51:45] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-11-20 08:51:45] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:51:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:54:46] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 08:54:46] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-11-20 08:54:51] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 08:57:52] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 08:57:52] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-11-20 08:57:57] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 09:00:58] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 09:00:58] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-11-20 09:00:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2024-11-20 09:00:59] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 09:00:59] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 09:00:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 09:00:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 09:00:59] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2024-11-20 09:00:59] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2024-11-20 09:00:59] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 09:00:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 09:04:00] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 09:04:00] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-11-20 09:04:05] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`

Example timings

gINTomics.Rcheck/gINTomics-Ex.timings

name	user	system	elapsed
create_multiassay	0.758	0.016	0.776
dot_plotly	0.597	0.004	0.603
extract_model_res	14.418	0.699	15.141
mirna_hsa	0.018	0.000	0.018
mmultiassay_ov	0.094	0.008	0.101
plot_chr_distribution	0.583	0.004	0.587
plot_heatmap	0.565	0.035	0.602
plot_network	0.581	0.033	0.614
plot_ridge	10.937	0.459	11.418
plot_tf_distribution	0.579	0.004	0.584
plot_venn	0.587	0.008	0.596