############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MAGeCKFlute ### ############################################################################## ############################################################################## * checking for file ‘MAGeCKFlute/DESCRIPTION’ ... OK * preparing ‘MAGeCKFlute’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘MAGeCKFlute.Rmd’ using rmarkdown snapshotDate(): 2022-06-29 ############################################################################## Pathview is an open source software package distributed under GNU General Public License version 3 (GPLv3). Details of GPLv3 is available at http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to formally cite the original Pathview paper (not just mention it) in publications or products. For details, do citation("pathview") within R. The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG license agreement (details at http://www.kegg.jp/kegg/legal.html). ############################################################################## clusterProfiler v4.5.1 For help: https://yulab-smu.top/biomedical-knowledge-mining-book/ If you use clusterProfiler in published research, please cite: T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141 Attaching package: 'clusterProfiler' The following object is masked from 'package:stats': filter Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider increasing max.overlaps Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider increasing max.overlaps 2022-07-06 23:38:44 # Running KEGG enrichment analysis 5 genes are mapped ... 2022-07-06 23:38:46 # Running KEGG enrichment analysis 10 genes are mapped ... Quitting from lines 278-288 (MAGeCKFlute.Rmd) Error: processing vignette 'MAGeCKFlute.Rmd' failed with diagnostics: Package "sva" is required. Please install it. --- failed re-building ‘MAGeCKFlute.Rmd’ --- re-building ‘MAGeCKFlute_enrichment.Rmd’ using rmarkdown 2022-07-06 23:38:52 # Running Pathway enrichment analysis 107 genes are mapped ... 2022-07-06 23:39:06 # Running KEGG enrichment analysis 54 genes are mapped ... 2022-07-06 23:39:09 # Running Pathway enrichment analysis 8561 genes are mapped ... preparing geneSet collections... GSEA analysis... leading edge analysis... done... 2022-07-06 23:39:54 # Running Complex enrichment analysis 9 genes are mapped ... 2022-07-06 23:39:56 # Running GOBP enrichment analysis 155 genes are mapped ... 2022-07-06 23:40:23 # Running Pathway enrichment analysis 107 genes are mapped ... --- finished re-building ‘MAGeCKFlute_enrichment.Rmd’ SUMMARY: processing the following file failed: ‘MAGeCKFlute.Rmd’ Error: Vignette re-building failed. Execution halted