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This page was generated on 2024-05-07 11:32:35 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4461
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 873/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.0.0  (landing page)
Angelo Velle
Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024)
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: RELEASE_3_19
git_last_commit: 6525a11
git_last_commit_date: 2024-04-30 11:56:24 -0400 (Tue, 30 Apr 2024)
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for gINTomics on kjohnson3


To the developers/maintainers of the gINTomics package:
- 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: gINTomics
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.0.0.tar.gz
StartedAt: 2024-05-06 21:54:12 -0400 (Mon, 06 May 2024)
EndedAt: 2024-05-06 22:08:06 -0400 (Mon, 06 May 2024)
EllapsedTime: 834.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: gINTomics.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/gINTomics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* this is package ‘gINTomics’ version ‘1.0.0’
* 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 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
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 21:55:30] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 21:55:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-06 21:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 21:55:30] [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:
  chr_cov cnv cnv_met coef cov Freq 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’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, 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’:

    expand.grid, I, 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-------------------
[2024-05-06 21:56:34] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-06 21:56:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 21:56:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 21:56:34] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-06 21:56:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 21:56:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 21:56:34] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-06 21:56:34] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-06 21:56:34] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 21:56:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 21:58:05] [WARN]    [OmnipathR] HTTP 504
[2024-05-06 21:58:05] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504
[2024-05-06 21:58:10] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 21:59:41] [WARN]    [OmnipathR] HTTP 504
[2024-05-06 21:59:41] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504
[2024-05-06 21:59:46] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 22:01:45] [WARN]    [OmnipathR] HTTP 504
[2024-05-06 22:01:45] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504
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 504
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:::import_omnipath(...)
  7. │           └─environment() %>% as.list %>% c(list(...)) %>% ...
  8. ├─OmnipathR:::omnipath_check_param(.)
  9. │ └─param$organisms %<>% map_int(ncbi_taxid)
 10. ├─purrr::map_int(., ncbi_taxid)
 11. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 12. │   ├─purrr:::with_indexed_errors(...)
 13. │   │ └─base::withCallingHandlers(...)
 14. │   ├─purrr:::call_with_cleanup(...)
 15. │   └─OmnipathR (local) .f(.x[[i]], ...)
 16. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 17. ├─purrr::map_int(., taxon_name, "ncbi")
 18. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 19. │   ├─purrr:::with_indexed_errors(...)
 20. │   │ └─base::withCallingHandlers(...)
 21. │   ├─purrr:::call_with_cleanup(...)
 22. │   └─OmnipathR (local) .f(.x[[i]], ...)
 23. │     ├─... %>% if_null_len0(NA)
 24. │     └─OmnipathR::get_db("organisms")
 25. │       └─OmnipathR::load_db(key, param = param)
 26. │         ├─rlang::exec(loader, !!!param)
 27. │         └─OmnipathR (local) `<fn>`()
 28. │           ├─... %>% ...
 29. │           └─OmnipathR::ensembl_organisms()
 30. │             ├─... %>% ...
 31. │             └─OmnipathR::ensembl_organisms_raw()
 32. │               └─... %>% html_table()
 33. ├─OmnipathR:::if_null_len0(., NA)
 34. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 35. ├─OmnipathR:::is_empty_2(.)
 36. │ └─value %>% ...
 37. ├─dplyr::first(.)
 38. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 39. │   └─vctrs::vec_size(x)
 40. ├─dplyr::pull(., name_type)
 41. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 42. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 43. ├─dplyr::mutate(...)
 44. ├─dplyr::full_join(...)
 45. ├─dplyr::mutate(...)
 46. ├─dplyr::select(...)
 47. ├─rvest::html_table(.)
 48. ├─rvest::html_element(., "table")
 49. ├─xml2::read_html(.)
 50. ├─OmnipathR:::download_to_cache(.)
 51. │ └─OmnipathR:::download_base(...)
 52. │   └─base::stop(result)
 53. └─purrr (local) `<fn>`(`<smplErrr>`)
 54.   └─cli::cli_abort(...)
 55.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 202 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-downloads.R:6:3'): .download_mirna_target works ────────────────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `map_int(., ncbi_taxid)`: i In index: 1.
  i With name: hsa.
  Caused by error in `map_int()`:
  i In index: 1.
  Caused by error:
  ! HTTP 504
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 202 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/gINTomics.Rcheck/00check.log’
for details.

Installation output

gINTomics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘gINTomics’ ...
** using staged installation
** R
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:45:54] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:45:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:45:54] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:00] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-06 15:46:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:00] [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
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:08] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:08] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:15] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-06 15:46:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 15:46:15] [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.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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(gINTomics)
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:01:51] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Contains 2 files.
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:01:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:01:51] [TRACE]   [OmnipathR] Cache locked: FALSE



> 
> test_check("gINTomics")
[2024-05-06 22:01:52] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-06 22:01:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:01:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:01:52] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-06 22:01:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:01:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:01:52] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-06 22:01:52] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-06 22:01:52] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 22:01:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 22:04:01] [WARN]    [OmnipathR] HTTP 504
[2024-05-06 22:04:01] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504
[2024-05-06 22:04:06] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 22:05:37] [WARN]    [OmnipathR] HTTP 504
[2024-05-06 22:05:37] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504
[2024-05-06 22:05:42] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 22:07:13] [WARN]    [OmnipathR] HTTP 504
[2024-05-06 22:07:13] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504
[2024-05-06 22:07:13] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-06 22:07:13] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-06 22:07:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:13] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-05-06 22:07:13] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-05-06 22:07:13] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 22:07:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] HTTP 200
[2024-05-06 22:07:33] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=2]
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:33] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 2: status changed from `unknown` to `ready`.
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-06 22:07:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:33] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-06 22:07:33] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-05-06 22:07:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-06 22:07:35] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:35] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-05-06 22:07:35] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:36] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-05-06 22:07:36] [INFO]    [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:36] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2024-05-06 22:07:36] [SUCCESS] [OmnipathR] Downloaded 3868 interactions.
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:36] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-05-06 22:07:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:38] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2024-05-06 22:07:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2024-05-06 22:07:38] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2024-05-06 22:07:38] [INFO]    [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2024-05-06 22:07:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-06 22:07:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-06 22:07:38] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2024-05-06 22:07:39] [SUCCESS] [OmnipathR] Downloaded 59469 interactions.
  2135 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:many mapping between keys and columns
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
Generating interactions
  2135 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.
'select()' returned 1:many mapping between keys and columns
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 202 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-downloads.R:6:3'): .download_mirna_target works ────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map_int(., ncbi_taxid)`: i In index: 1.
i With name: hsa.
Caused by error in `map_int()`:
i In index: 1.
Caused by error:
! HTTP 504

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 202 ]
Error: Test failures
Execution halted

Example timings

gINTomics.Rcheck/gINTomics-Ex.timings

nameusersystemelapsed
create_multiassay0.1700.0090.178
dot_plotly0.1580.0060.164
extract_model_res3.9810.1024.085
mirna_hsa0.0050.0000.006
mmultiassay_ov0.0430.0010.044
plot_chr_distribution0.1470.0070.153
plot_heatmap0.1480.0060.155
plot_network0.1540.0080.161
plot_ridge2.8160.1042.920
plot_tf_distribution0.1340.0060.140
plot_venn0.1420.0080.150