##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings metaseqR2_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/metaseqR2.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.19.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 45 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘metaseqR2’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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
getUcscUtr: no visible binding for global variable ‘customDir’
Undefined global functions or variables:
  customDir
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  metaseqr2.Rd: render
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘metaseqR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAnnotation
> ### Title: Annotation downloader
> ### Aliases: getAnnotation
> 
> ### ** Examples
> 
> mm10Genes <- getAnnotation("mm10","gene")
Using Ensembl host https://jan2024.archive.ensembl.org
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─metaseqR2::getAnnotation("mm10", "gene")
  2.   └─metaseqR2:::getEnsemblAnnotation(org, type, ver)
  3.     └─biomaRt::useMart(biomart = dat, host = host, dataset = getDataset(org))
  4.       └─biomaRt:::.useMart(...)
  5.         └─biomaRt:::.listMarts(...)
  6.           └─biomaRt:::bmRequest(...)
  7.             └─httr2::req_perform(request)
  8.               └─httr2:::handle_resp(req, resp, error_call = error_call)
  9.                 └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 10.                   ├─rlang::catch_cnd(...)
 11.                   │ ├─rlang::eval_bare(...)
 12.                   │ ├─base::tryCatch(...)
 13.                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 16.                   │ └─base::force(expr)
 17.                   └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  metaseqR2 RUnit Tests - 2 test functions, 1 error, 0 failures
  ERROR in test_estimate_aufc_weights: Error in req_perform(request) : HTTP 500 Internal Server Error.
  
  Test files with failing tests
  
     test_estimate_aufc_weights.R 
       test_estimate_aufc_weights 
  
  
  Error in BiocGenerics:::testPackage("metaseqR2") : 
    unit tests failed for package metaseqR2
  In addition: Warning message:
  The column that contains the gene biotypes ("embedCols$btCol") is missing with embedded annotation! Biotype filters and certain plots will not be available... 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘metaseqr2-annotation.Rmd’ using rmarkdown

Quitting from metaseqr2-annotation.Rmd:107-122 [example-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metaseqr2-annotation.Rmd' failed with diagnostics:
HTTP 500 Internal Server Error.
--- failed re-building ‘metaseqr2-annotation.Rmd’

--- re-building ‘metaseqr2-statistics.Rmd’ using rmarkdown
  adding: tmp/RtmpHIh0X2/test1/plots/qc/correlation_correlogram.png (deflated 1%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/correlation_heatmap.png (deflated 9%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/correlation_pairs.png (deflated 1%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/filtered_genes.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/mds.png (deflated 44%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/boxplot_normalized.png (deflated 17%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/boxplot_raw.png (deflated 17%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/gcbias_normalized.png (deflated 13%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/gcbias_raw.png (deflated 12%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/lengthbias_normalized.png (deflated 10%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/lengthbias_raw.png (deflated 10%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meanvar_normalized.png (deflated 6%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meanvar_raw.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 6%)
  adding: tmp/RtmpHIh0X2/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 7%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: tmp/RtmpHIh0X2/test1/plots/qc/mds.pdf (deflated 12%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/boxplot_normalized.pdf (deflated 12%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/gcbias_normalized.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/gcbias_raw.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/lengthbias_normalized.pdf (deflated 1%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/lengthbias_raw.pdf (deflated 1%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 21%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 21%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meanvar_normalized.pdf (deflated 44%)
  adding: tmp/RtmpHIh0X2/test1/plots/normalization/meanvar_raw.pdf (deflated 39%)
  adding: tmp/RtmpHIh0X2/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 9%)
  adding: tmp/RtmpHIh0X2/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
  adding: tmp/RtmpHIh0X2/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
  adding: tmp/RtmpHIh0X2/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.pdf (deflated 2%)
trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://code.highcharts.com/highcharts.js'
downloaded 268 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 92 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 19 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 26 KB

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
Content type 'text/javascript' length 56670 bytes (55 KB)
==================================================
downloaded 55 KB

  adding: tmp/RtmpHIh0X2/test2/plots/qc/correlation_correlogram.png (deflated 1%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/correlation_heatmap.png (deflated 9%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/correlation_pairs.png (deflated 1%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/filtered_genes.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/mds.png (deflated 44%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/boxplot_normalized.png (deflated 12%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/boxplot_raw.png (deflated 17%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/gcbias_normalized.png (deflated 20%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/gcbias_raw.png (deflated 12%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/lengthbias_normalized.png (deflated 11%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/lengthbias_raw.png (deflated 10%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meanvar_normalized.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meanvar_raw.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 6%)
  adding: tmp/RtmpHIh0X2/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test2/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test2/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 13%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: tmp/RtmpHIh0X2/test2/plots/qc/mds.pdf (deflated 12%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/boxplot_normalized.pdf (deflated 8%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/gcbias_normalized.pdf (deflated 6%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/gcbias_raw.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/lengthbias_normalized.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/lengthbias_raw.pdf (deflated 1%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 33%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 33%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meanvar_normalized.pdf (deflated 40%)
  adding: tmp/RtmpHIh0X2/test2/plots/normalization/meanvar_raw.pdf (deflated 39%)
  adding: tmp/RtmpHIh0X2/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 10%)
  adding: tmp/RtmpHIh0X2/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
  adding: tmp/RtmpHIh0X2/test2/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
  adding: tmp/RtmpHIh0X2/test2/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.pdf (deflated 2%)
trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://code.highcharts.com/highcharts.js'
downloaded 268 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 92 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 19 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 26 KB

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
Content type 'text/javascript' length 56670 bytes (55 KB)
==================================================
downloaded 55 KB

  adding: tmp/RtmpHIh0X2/test3/plots/qc/correlation_correlogram.png (deflated 1%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/correlation_heatmap.png (deflated 9%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/correlation_pairs.png (deflated 1%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/filtered_genes.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/mds.png (deflated 44%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/boxplot_normalized.png (deflated 18%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/boxplot_raw.png (deflated 17%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/gcbias_normalized.png (deflated 13%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/gcbias_raw.png (deflated 12%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/lengthbias_normalized.png (deflated 10%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/lengthbias_raw.png (deflated 10%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 4%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 4%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meanvar_normalized.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meanvar_raw.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 6%)
  adding: tmp/RtmpHIh0X2/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test3/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test3/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 11%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: tmp/RtmpHIh0X2/test3/plots/qc/mds.pdf (deflated 12%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/boxplot_normalized.pdf (deflated 12%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/gcbias_normalized.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/gcbias_raw.pdf (deflated 4%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/lengthbias_normalized.pdf (deflated 2%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/lengthbias_raw.pdf (deflated 1%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 21%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 21%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meanvar_normalized.pdf (deflated 30%)
  adding: tmp/RtmpHIh0X2/test3/plots/normalization/meanvar_raw.pdf (deflated 39%)
  adding: tmp/RtmpHIh0X2/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 10%)
  adding: tmp/RtmpHIh0X2/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
  adding: tmp/RtmpHIh0X2/test3/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
  adding: tmp/RtmpHIh0X2/test3/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.pdf (deflated 2%)
trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://code.highcharts.com/highcharts.js'
downloaded 268 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 92 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 19 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 26 KB

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
Content type 'text/javascript' length 56670 bytes (55 KB)
==================================================
downloaded 55 KB

  adding: tmp/RtmpHIh0X2/test4/plots/qc/correlation_correlogram.png (deflated 1%)
  adding: tmp/RtmpHIh0X2/test4/plots/qc/correlation_heatmap.png (deflated 9%)
  adding: tmp/RtmpHIh0X2/test4/plots/qc/correlation_pairs.png (deflated 1%)
  adding: tmp/RtmpHIh0X2/test4/plots/qc/filtered_genes.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test4/plots/qc/mds.png (deflated 44%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/boxplot_normalized.png (deflated 18%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/boxplot_raw.png (deflated 17%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/gcbias_normalized.png (deflated 13%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/gcbias_raw.png (deflated 12%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/lengthbias_normalized.png (deflated 10%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/lengthbias_raw.png (deflated 10%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 4%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 4%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 3%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/meanvar_normalized.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test4/plots/normalization/meanvar_raw.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test4/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 6%)
  adding: tmp/RtmpHIh0X2/test4/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 5%)
  adding: tmp/RtmpHIh0X2/test4/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 4%)
  adding: tmp/RtmpHIh0X2/test4/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 12%)
trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://code.highcharts.com/highcharts.js'
downloaded 268 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 92 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 19 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 26 KB

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
Content type 'text/javascript' length 56670 bytes (55 KB)
==================================================
downloaded 55 KB


Quitting from metaseqr2-statistics.Rmd:437-446 [example-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metaseqr2-statistics.Rmd' failed with diagnostics:
HTTP 500 Internal Server Error.
--- failed re-building ‘metaseqr2-statistics.Rmd’

SUMMARY: processing the following files failed:
  ‘metaseqr2-annotation.Rmd’ ‘metaseqr2-statistics.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.