############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2 ### ############################################################################## ############################################################################## * checking for file ‘metaseqR2/DESCRIPTION’ ... OK * preparing ‘metaseqR2’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘metaseqr2-annotation.Rmd’ using rmarkdown --- finished re-building ‘metaseqr2-annotation.Rmd’ --- re-building ‘metaseqr2-statistics.Rmd’ using rmarkdown 2025-03-21 02:46:27.785 R[82003:310603411] XType: Using static font registry. Warning: call dbDisconnect() when finished working with a connection adding: tmp/RtmpPbfgph/test1/plots/qc/correlation_correlogram.png (deflated 2%) adding: tmp/RtmpPbfgph/test1/plots/qc/correlation_heatmap.png (deflated 16%) adding: tmp/RtmpPbfgph/test1/plots/qc/correlation_pairs.png (deflated 1%) adding: tmp/RtmpPbfgph/test1/plots/qc/filtered_genes.png (deflated 6%) adding: tmp/RtmpPbfgph/test1/plots/qc/mds.png (deflated 45%) adding: tmp/RtmpPbfgph/test1/plots/normalization/boxplot_normalized.png (deflated 19%) adding: tmp/RtmpPbfgph/test1/plots/normalization/boxplot_raw.png (deflated 15%) adding: tmp/RtmpPbfgph/test1/plots/normalization/gcbias_normalized.png (deflated 12%) adding: tmp/RtmpPbfgph/test1/plots/normalization/gcbias_raw.png (deflated 12%) adding: tmp/RtmpPbfgph/test1/plots/normalization/lengthbias_normalized.png (deflated 9%) adding: tmp/RtmpPbfgph/test1/plots/normalization/lengthbias_raw.png (deflated 8%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 5%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 5%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meanvar_normalized.png (deflated 11%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meanvar_raw.png (deflated 8%) adding: tmp/RtmpPbfgph/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 10%) adding: tmp/RtmpPbfgph/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 9%) adding: tmp/RtmpPbfgph/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%) adding: tmp/RtmpPbfgph/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 6%) adding: tmp/RtmpPbfgph/test1/plots/qc/correlation_correlogram.pdf (deflated 4%) adding: tmp/RtmpPbfgph/test1/plots/qc/correlation_heatmap.pdf (deflated 26%) adding: tmp/RtmpPbfgph/test1/plots/qc/correlation_pairs.pdf (deflated 4%) adding: tmp/RtmpPbfgph/test1/plots/qc/filtered_genes.pdf (deflated 7%) adding: tmp/RtmpPbfgph/test1/plots/qc/mds.pdf (deflated 12%) adding: tmp/RtmpPbfgph/test1/plots/normalization/boxplot_normalized.pdf (deflated 12%) adding: tmp/RtmpPbfgph/test1/plots/normalization/boxplot_raw.pdf (deflated 12%) adding: tmp/RtmpPbfgph/test1/plots/normalization/gcbias_normalized.pdf (deflated 4%) adding: tmp/RtmpPbfgph/test1/plots/normalization/gcbias_raw.pdf (deflated 4%) adding: tmp/RtmpPbfgph/test1/plots/normalization/lengthbias_normalized.pdf (deflated 1%) adding: tmp/RtmpPbfgph/test1/plots/normalization/lengthbias_raw.pdf (deflated 1%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 21%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 21%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meanvar_normalized.pdf (deflated 44%) adding: tmp/RtmpPbfgph/test1/plots/normalization/meanvar_raw.pdf (deflated 39%) adding: tmp/RtmpPbfgph/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 9%) adding: tmp/RtmpPbfgph/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%) adding: tmp/RtmpPbfgph/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%) adding: tmp/RtmpPbfgph/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 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js' Quitting from metaseqr2-statistics.Rmd:228-284 [example-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `download.file()`: ! cannot open URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js' --- Backtrace: ▆ 1. └─metaseqR2::metaseqr2(...) 2. └─metaseqR2:::.downloadJsLibs(PROJECT_PATH, reportDb) 3. └─utils::download.file(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'metaseqr2-statistics.Rmd' failed with diagnostics: cannot open URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js' --- failed re-building ‘metaseqr2-statistics.Rmd’ SUMMARY: processing the following file failed: ‘metaseqr2-statistics.Rmd’ Error: Vignette re-building failed. Execution halted