Vignette building failed during fgcz installation

[Tilias]

Vignettes building, using the following command fails:

devtools::install_github("protViz/fgcz.gsea.ora", build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE, force = TRUE)

giving error:

Error: Failed to install 'fgcz.gsea.ora' from GitHub:
  System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
E> 
E> Error: processing vignette 'vignette.Rmd' failed with diagnostics:
E> LaTeX failed to compile C:/Users/liepa/AppData/Local/Temp/RtmpiEmWlb/Rbuild1e0c461443e6/fgcz.gsea.ora/vignettes/vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette.log for more info.
E> --- failed re-building 'vignette.Rmd'
E> 
E> SUMMARY: processing the following file failed:
E>   'vignette.Rmd'
E> 
E> Error: Vignette re-building failed.
E> Execution halted

[Witold Wolski]

Did you had look at the "vignette.log"?

[lisajohanna]

On my computer (windows) it works when I do

• library(devtools)
• install_github("protViz/fgcz.gsea.ora", build_vignettes = TRUE, force = TRUE)

not sure if it is different for Linux or Mac

[Tilias]

devtools::build_vignettes()

gives error:

Building fgcz.gsea.ora vignettes
--- re-building 'vignette.Rmd' using rmarkdown
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Joining, by = "pathwayID"
Garbage collection 83 = 63+8+12 (level 2) ... 
205.7 Mbytes of cons cells used (56%)
127.7 Mbytes of vectors used (16%)
Garbage collection 152 = 128+10+14 (level 2) ... 
205.8 Mbytes of cons cells used (56%)
77.7 Mbytes of vectors used (15%)
Garbage collection 153 = 128+10+15 (level 2) ... 
205.8 Mbytes of cons cells used (56%)
77.0 Mbytes of vectors used (19%)
Garbage collection 154 = 128+10+16 (level 2) ... 
205.8 Mbytes of cons cells used (56%)
77.0 Mbytes of vectors used (24%)
Garbage collection 155 = 128+10+17 (level 2) ... 
205.8 Mbytes of cons cells used (56%)
77.0 Mbytes of vectors used (30%)
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
! LaTeX Error: Missing \begin{document}.

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
LaTeX failed to compile C:/Users/liepa/Documents/fgcz/fgcz.gsea.ora/vignettes/vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See vignette.log for more info.
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error : Vignette re-building failed.
Error: callr subprocess failed: Vignette re-building failed.

Session info

sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_Switzerland.1252  LC_CTYPE=English_Switzerland.1252   
[3] LC_MONETARY=English_Switzerland.1252 LC_NUMERIC=C                        
[5] LC_TIME=English_Switzerland.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] fgcz.gsea.ora_0.1.0 WebGestaltR_0.4.3   forcats_0.5.0      
 [4] stringr_1.4.0       dplyr_0.8.5         purrr_0.3.3        
 [7] readr_1.3.1         tidyr_1.0.2         tibble_2.1.3       
[10] ggplot2_3.3.0       tidyverse_1.3.0     BiocStyle_2.14.4   

loaded via a namespace (and not attached):
 [1] colorspace_1.4-1     ellipsis_0.3.0       rprojroot_1.3-2     
 [4] fs_1.3.2             rstudioapi_0.11      remotes_2.1.1       
 [7] bit64_0.9-7          AnnotationDbi_1.48.0 fansi_0.4.1         
[10] lubridate_1.7.4      xml2_1.2.5           codetools_0.2-16    
[13] doParallel_1.0.15    knitr_1.28           pkgload_1.0.2       
[16] jsonlite_1.6.1       apcluster_1.4.8      broom_0.5.5         
[19] GO.db_3.10.0         dbplyr_1.4.2         BiocManager_1.30.10 
[22] compiler_3.6.2       httr_1.4.1           backports_1.1.5     
[25] assertthat_0.2.1     Matrix_1.2-18        cli_2.0.2           
[28] htmltools_0.4.0      prettyunits_1.1.1    tools_3.6.2         
[31] igraph_1.2.4.2       gtable_0.3.0         glue_1.3.2          
[34] doRNG_1.8.2          tinytex_0.20         Rcpp_1.0.4          
[37] slam_0.1-47          Biobase_2.46.0       cellranger_1.1.0    
[40] vctrs_0.2.4          svglite_1.2.3        nlme_3.1-142        
[43] iterators_1.0.12     sigora_3.0.5         xfun_0.12           
[46] ps_1.3.2             testthat_2.3.2       rvest_0.3.5         
[49] lifecycle_0.2.0      rngtools_1.5         devtools_2.2.2      
[52] org.Hs.eg.db_3.10.0  scales_1.1.0         reactome.db_1.70.0  
[55] hms_0.5.3            parallel_3.6.2       yaml_2.2.1          
[58] memoise_1.1.0        gridExtra_2.3        UpSetR_1.4.0        
[61] gdtools_0.2.1        stringi_1.4.6        RSQLite_2.2.0       
[64] S4Vectors_0.24.3     desc_1.2.0           foreach_1.4.8       
[67] BiocGenerics_0.32.0  pkgbuild_1.0.6       rlang_0.4.5         
[70] pkgconfig_2.0.3      systemfonts_0.1.1    evaluate_0.14       
[73] lattice_0.20-38      bit_1.1-15.2         processx_3.4.2      
[76] tidyselect_1.0.0     plyr_1.8.6           magrittr_1.5        
[79] R6_2.4.1             IRanges_2.20.2       generics_0.0.2      
[82] DBI_1.1.0            pillar_1.4.3         haven_2.2.0         
[85] whisker_0.4          withr_2.1.2          modelr_0.1.6        
[88] crayon_1.3.4         rmarkdown_2.1        usethis_1.5.1       
[91] grid_3.6.2           readxl_1.3.1         blob_1.2.1          
[94] callr_3.4.2          reprex_0.3.0         digest_0.6.25       
[97] stats4_3.6.2         munsell_0.5.0        sessioninfo_1.1.1