##############################################################################
##############################################################################
###
### 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.