Panagiotis Moulos
| Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/metaseqR2 |
| git_branch: devel |
| git_last_commit: eebcb8e |
| git_last_commit_date: 2023-10-24 11:22:10 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:39:29 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 1200/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metaseqR2 1.15.0 (landing page) Panagiotis Moulos
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the metaseqR2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaseqR2.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. |
| Package: metaseqR2 |
| Version: 1.15.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2 |
| StartedAt: 2024-03-01 20:19:41 -0500 (Fri, 01 Mar 2024) |
| EndedAt: 2024-03-01 20:34:45 -0500 (Fri, 01 Mar 2024) |
| EllapsedTime: 903.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### 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
Failed with error: 'unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RMySQL/libs/RMySQL.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RMySQL/libs/RMySQL.so, 0x0006): Library not loaded: '@loader_path/../../../../opt/openssl@3/lib/libssl.3.dylib'
Referenced from: '/usr/local/Cellar/mysql/8.1.0/lib/libmysqlclient.22.dylib'
Reason: tried: '/usr/local/Cellar/mysql/8.1.0/lib/../../../../opt/openssl@3/lib/libssl.3.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libssl.3.dylib' (no such file), '/usr/local/jdk-21.jdk/Contents/Home/lib/server/libssl.3.dylib' (no such file)'
Quitting from lines 132-153 [example-2] (metaseqr2-annotation.Rmd)
Error: processing vignette 'metaseqr2-annotation.Rmd' failed with diagnostics:
cannot open URL 'http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/ensemblSource.txt.gz'
--- failed re-building ‘metaseqr2-annotation.Rmd’
--- re-building ‘metaseqr2-statistics.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
2024-03-01 20:26:19.404 R[81977:911573776] XType: com.apple.fonts is not accessible.
2024-03-01 20:26:19.409 R[81977:911573776] XType: XTFontStaticRegistry is enabled.
adding: tmp/RtmpuuE8pf/test1/plots/qc/correlation_correlogram.png (deflated 2%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/correlation_heatmap.png (deflated 16%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/correlation_pairs.png (deflated 1%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/filtered_genes.png (deflated 6%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/mds.png (deflated 48%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/boxplot_normalized.png (deflated 19%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/boxplot_raw.png (deflated 15%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/gcbias_normalized.png (deflated 12%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/gcbias_raw.png (deflated 12%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/lengthbias_normalized.png (deflated 9%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/lengthbias_raw.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meanvar_normalized.png (deflated 11%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meanvar_raw.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 10%)
adding: tmp/RtmpuuE8pf/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 9%)
adding: tmp/RtmpuuE8pf/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 6%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/correlation_correlogram.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/correlation_heatmap.pdf (deflated 26%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/correlation_pairs.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/filtered_genes.pdf (deflated 7%)
adding: tmp/RtmpuuE8pf/test1/plots/qc/mds.pdf (deflated 12%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/boxplot_normalized.pdf (deflated 12%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/boxplot_raw.pdf (deflated 12%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/gcbias_normalized.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/gcbias_raw.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/lengthbias_normalized.pdf (deflated 1%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/lengthbias_raw.pdf (deflated 1%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 21%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 21%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meanvar_normalized.pdf (deflated 44%)
adding: tmp/RtmpuuE8pf/test1/plots/normalization/meanvar_raw.pdf (deflated 39%)
adding: tmp/RtmpuuE8pf/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 9%)
adding: tmp/RtmpuuE8pf/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
adding: tmp/RtmpuuE8pf/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
adding: tmp/RtmpuuE8pf/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 271 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 9675 bytes
trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'
Content type 'text/javascript' length 35122 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js'
Content type 'text/javascript' length 100524 bytes (98 KB)
==================================================
downloaded 98 KB
trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
downloaded 55 KB
adding: tmp/RtmpuuE8pf/test2/plots/qc/correlation_correlogram.png (deflated 2%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/correlation_heatmap.png (deflated 16%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/correlation_pairs.png (deflated 1%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/filtered_genes.png (deflated 7%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/mds.png (deflated 48%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/boxplot_normalized.png (deflated 14%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/boxplot_raw.png (deflated 15%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/gcbias_normalized.png (deflated 22%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/gcbias_raw.png (deflated 12%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/lengthbias_normalized.png (deflated 14%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/lengthbias_raw.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meanvar_normalized.png (deflated 11%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meanvar_raw.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 10%)
adding: tmp/RtmpuuE8pf/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 9%)
adding: tmp/RtmpuuE8pf/test2/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test2/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 14%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/correlation_correlogram.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/correlation_heatmap.pdf (deflated 26%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/correlation_pairs.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/filtered_genes.pdf (deflated 7%)
adding: tmp/RtmpuuE8pf/test2/plots/qc/mds.pdf (deflated 12%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/boxplot_normalized.pdf (deflated 8%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/boxplot_raw.pdf (deflated 12%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/gcbias_normalized.pdf (deflated 6%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/gcbias_raw.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/lengthbias_normalized.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/lengthbias_raw.pdf (deflated 1%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 33%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 33%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meanvar_normalized.pdf (deflated 40%)
adding: tmp/RtmpuuE8pf/test2/plots/normalization/meanvar_raw.pdf (deflated 39%)
adding: tmp/RtmpuuE8pf/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 10%)
adding: tmp/RtmpuuE8pf/test2/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
adding: tmp/RtmpuuE8pf/test2/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
adding: tmp/RtmpuuE8pf/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 271 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 9675 bytes
trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'
Content type 'text/javascript' length 35122 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js'
Content type 'text/javascript' length 100524 bytes (98 KB)
==================================================
downloaded 98 KB
trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
downloaded 55 KB
adding: tmp/RtmpuuE8pf/test3/plots/qc/correlation_correlogram.png (deflated 2%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/correlation_heatmap.png (deflated 16%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/correlation_pairs.png (deflated 1%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/filtered_genes.png (deflated 7%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/mds.png (deflated 48%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/boxplot_normalized.png (deflated 24%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/boxplot_raw.png (deflated 15%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/gcbias_normalized.png (deflated 13%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/gcbias_raw.png (deflated 12%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/lengthbias_normalized.png (deflated 10%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/lengthbias_raw.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meanvar_normalized.png (deflated 7%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meanvar_raw.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 10%)
adding: tmp/RtmpuuE8pf/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 9%)
adding: tmp/RtmpuuE8pf/test3/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test3/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 13%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/correlation_correlogram.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/correlation_heatmap.pdf (deflated 26%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/correlation_pairs.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/filtered_genes.pdf (deflated 7%)
adding: tmp/RtmpuuE8pf/test3/plots/qc/mds.pdf (deflated 12%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/boxplot_normalized.pdf (deflated 12%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/boxplot_raw.pdf (deflated 12%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/gcbias_normalized.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/gcbias_raw.pdf (deflated 4%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/lengthbias_normalized.pdf (deflated 2%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/lengthbias_raw.pdf (deflated 1%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 21%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 21%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meanvar_normalized.pdf (deflated 30%)
adding: tmp/RtmpuuE8pf/test3/plots/normalization/meanvar_raw.pdf (deflated 39%)
adding: tmp/RtmpuuE8pf/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 10%)
adding: tmp/RtmpuuE8pf/test3/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
adding: tmp/RtmpuuE8pf/test3/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
adding: tmp/RtmpuuE8pf/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 271 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 9675 bytes
trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'
Content type 'text/javascript' length 35122 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js'
Content type 'text/javascript' length 100524 bytes (98 KB)
==================================================
downloaded 98 KB
trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
downloaded 55 KB
adding: tmp/RtmpuuE8pf/test4/plots/qc/correlation_correlogram.png (deflated 2%)
adding: tmp/RtmpuuE8pf/test4/plots/qc/correlation_heatmap.png (deflated 16%)
adding: tmp/RtmpuuE8pf/test4/plots/qc/correlation_pairs.png (deflated 1%)
adding: tmp/RtmpuuE8pf/test4/plots/qc/filtered_genes.png (deflated 7%)
adding: tmp/RtmpuuE8pf/test4/plots/qc/mds.png (deflated 48%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/boxplot_normalized.png (deflated 24%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/boxplot_raw.png (deflated 15%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/gcbias_normalized.png (deflated 13%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/gcbias_raw.png (deflated 12%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/lengthbias_normalized.png (deflated 10%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/lengthbias_raw.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 5%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/meanvar_normalized.png (deflated 7%)
adding: tmp/RtmpuuE8pf/test4/plots/normalization/meanvar_raw.png (deflated 8%)
adding: tmp/RtmpuuE8pf/test4/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 10%)
adding: tmp/RtmpuuE8pf/test4/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 9%)
adding: tmp/RtmpuuE8pf/test4/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%)
adding: tmp/RtmpuuE8pf/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 271 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 9675 bytes
trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'
Content type 'text/javascript' length 35122 bytes (34 KB)
==================================================
downloaded 34 KB
trying URL 'http://jvenn.toulouse.inrae.fr/app/js/jvenn.min.js'
Content type 'text/javascript' length 100524 bytes (98 KB)
==================================================
downloaded 98 KB
trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
downloaded 55 KB
statEdger package:metaseqR2 R Documentation
_S_t_a_t_i_s_t_i_c_a_l _t_e_s_t_i_n_g _w_i_t_h _e_d_g_e_R
_D_e_s_c_r_i_p_t_i_o_n:
This function is a wrapper over edgeR statistical testing. It
accepts a matrix of normalized gene counts or an S4 object
specific to each normalization algorithm supported by metaseqR2.
_U_s_a_g_e:
statEdger(object, sampleList, contrastList = NULL,
statArgs = NULL)
_A_r_g_u_m_e_n_t_s:
object: a matrix or an object specific to each normalization
algorithm supported by metaseqR2, containing normalized
counts. See also Details.
sampleList: the list containing condition names and the samples under
each condition.
contrastList: vector of contrasts as defined in the main help page of
'metaseqr2'. See also Details.
statArgs: a list of edgeR statistical algorithm parameters. See the
result of 'getDefaults("statistics",' '"edger")' for an
example and how you can modify it.
_D_e_t_a_i_l_s:
Regarding 'object', apart from 'matrix' (also for NOISeq), the
object can be a 'SeqExpressionSet' (EDASeq), 'CountDataSet'
(DESeq), 'DGEList' (edgeR), 'DESeqDataSet' (DESeq2), 'SeqCountSet'
(DSS) or 'ABSDataSet' (ABSSeq).
Regarding 'contrastList' it can also be a named structured list of
contrasts as returned by the internal function
'metaseqR2:::makeContrastList'.
_V_a_l_u_e:
A named list of p-values, whose names are the names of the
contrasts.
_A_u_t_h_o_r(_s):
Panagiotis Moulos
_E_x_a_m_p_l_e_s:
require(edgeR)
dataMatrix <- metaseqR2:::exampleCountData(2000)
sampleList <- list(A=c("A1","A2"),B=c("B1","B2","B3"))
contrast <- "A_vs_B"
normDataMatrix <- normalizeEdger(dataMatrix,sampleList)
p <- statEdger(normDataMatrix,sampleList,contrast)
--- finished re-building ‘metaseqr2-statistics.Rmd’
SUMMARY: processing the following file failed:
‘metaseqr2-annotation.Rmd’
Error: Vignette re-building failed.
Execution halted