vignettes causing errors in GHA (but not locally)

[bschilder]

Might be related to "print" issues:
r-lib/actions#319 (comment)
r-lib/devtools#2407

[bschilder]

Even using the "--no-vignettes" flag during R checks produces the errors:

Loading required package: rcmdcheck
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file 'D:\a\echolocatoR\echolocatoR/DESCRIPTION' ... OK
* preparing 'echolocatoR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building 'QTLs.Rmd' using rmarkdown
Quitting from lines 74-83 (QTLs.Rmd) 
Error: Error: processing vignette 'QTLs.Rmd' failed with diagnostics:
'CreateProcess' failed to run 'C:\Users\RUNNER~1\AppData\Local\R\cache\R\ECHOFI~1\FINEMAP\FINEMA~1.1_X\FINEMA~1.1_X -h'
--- failed re-building 'QTLs.Rmd'
--- re-building 'docker.Rmd' using rmarkdown
--- finished re-building 'docker.Rmd'
--- re-building 'echolocatoR.Rmd' using rmarkdown
Quitting from lines 85-95 (echolocatoR.Rmd) 
Error: Error: processing vignette 'echolocatoR.Rmd' failed with diagnostics:
Must provide a valid target_path.
--- failed re-building 'echolocatoR.Rmd'
--- re-building 'finemapping_portal.Rmd' using rmarkdown
Downloading: https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/ASXL3/multi_finemap/ASXL3.UKB.multi_finemap.csv.gz
trying URL 'https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/ASXL3/multi_finemap/ASXL3.UKB.multi_finemap.csv.gz'
Content type 'application/octet-stream' length 157348 bytes (153 KB)
==================================================
downloaded 153 KB
Downloading: https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/BIN3/multi_finemap/BIN3.UKB.multi_finemap.csv.gz
trying URL 'https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/BIN3/multi_finemap/BIN3.UKB.multi_finemap.csv.gz'
Content type 'application/octet-stream' length 230370 bytes (224 KB)
==================================================
downloaded 224 KB
Downloading: https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/ASXL3/LD/ASXL3.UKB.LD.csv.gz
trying URL 'https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/ASXL3/LD/ASXL3.UKB.LD.csv.gz'
Content type 'application/octet-stream' length 66098 bytes (64 KB)
==================================================
downloaded 64 KB
Downloading: https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/BIN3/LD/BIN3.UKB.LD.csv.gz
trying URL 'https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/BIN3/LD/BIN3.UKB.LD.csv.gz'
Content type 'application/octet-stream' length 100237 bytes (97 KB)
==================================================
downloaded 97 KB
--- finished re-building 'finemapping_portal.Rmd'
--- re-building 'summarise.Rmd' using rmarkdown
The magick package is required to crop "C:/Users/runneradmin/AppData/Local/Temp/RtmpAbYNk3/Rbuild5e81f88ea1/echolocatoR/vignettes/summarise_files/figure-html/super_summary_plot()-1.png" but not available.
--- finished re-building 'summarise.Rmd'
SUMMARY: processing the following files failed:
  'QTLs.Rmd' 'echolocatoR.Rmd'
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.
Run actions/upload-artifact@v2
Warning: No files were found with the provided path: check. No artifacts will be uploaded.

[bschilder]

Thought it might be related to the RGL_USE_NULL variable, but setting this var in the global env and then passing it to the R CMD step didnt seem to help:
r-lib/remotes#332

Supporting the idea that this is unrelated, couldn't find any error messages relating to RGL, e.g.
Error : package ‘rgl’ could not be loaded

[bschilder]

Looks like theres two main issues here.

QTL.Rmd

Error: --- re-building 'QTLs.Rmd' using rmarkdown
Quitting from lines 74-83 (QTLs.Rmd) 
Error: Error: processing vignette 'QTLs.Rmd' failed with diagnostics:
'CreateProcess' failed to run 'C:\Users\RUNNER~1\AppData\Local\R\cache\R\ECHOFI~1\FINEMAP\FINEMA~1.1_X\FINEMA~1.1_X -h'

I think the "~" might just be indicating an abbreviated path rather than an actual typo.

echolocatoR.Rmd

Quitting from lines 85-95 (echolocatoR.Rmd) 
Error: Error: processing vignette 'echolocatoR.Rmd' failed with diagnostics:
Must provide a valid target_path.

[bschilder]

Another error coming up in Linux Docker checks (but not when running in R console on Linux, nor when i run checks in Rstudio on my Mac):

Error in `grid.newpage()`: could not open file '/tmp/RtmpR72AYX/working_dir/Rtmpz2f6Oo/results/GWAS/Nalls23andMe_2019/BST1/multiview.BST1./usr/local/lib/R/site-library/echodata/extdata/BST1.1KGphase3.vcf.bgz.1x.png'
Backtrace:
    ▆
 1. └─echolocatoR::finemap_loci(...) at test-finemap_loci.R:77:2
 2.   └─base::lapply(...)
 3.     └─echolocatoR (local) FUN(X[[i]], ...)
 4.       └─base::tryCatch(...)
 5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.             └─value[[3L]](cond)

[ FAIL 1 | WARN 28 | SKIP 1 | PASS 28 ]
Error: Test failures
Execution halted

Seems similar to these issues in ggplot2. I've heard through the Bioc developers mailing list there may be some issues with ggplot2's latest release as well:
tidyverse/ggplot2#2917
https://stackoverflow.com/questions/41307384/errors-warnings-when-running-ggplots

Session info

R Under development (unstable) (2022-11-07 r83308)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] snpStats_1.49.0   Matrix_1.5-3      survival_3.4-0    echolocatoR_2.0.3

loaded via a namespace (and not attached):
  [1] ProtGenerics_1.31.0         fs_1.5.2                   
  [3] matrixStats_0.62.0          bitops_1.0-7               
  [5] EnsDb.Hsapiens.v75_2.99.0   devtools_2.4.5             
  [7] httr_1.4.4                  RColorBrewer_1.1-3         
  [9] Rgraphviz_2.43.0            profvis_0.3.7              
 [11] tools_4.3.0                 backports_1.4.1            
 [13] utf8_1.2.2                  R6_2.5.1                   
 [15] DT_0.26                     lazyeval_0.2.2             
 [17] urlchecker_1.0.1            withr_2.5.0                
 [19] prettyunits_1.1.1           GGally_2.1.2               
 [21] gridExtra_2.3               textshaping_0.3.6          
 [23] cli_3.4.1                   Biobase_2.59.0             
 [25] labeling_0.4.2              ggbio_1.47.0               
 [27] mvtnorm_1.1-3               readr_2.1.3                
 [29] proxy_0.4-27                mixsqp_0.3-43              
 [31] systemfonts_1.0.4           Rsamtools_2.15.0           
 [33] foreign_0.8-83              R.utils_2.12.2             
 [35] dichromat_2.0-0.1           sessioninfo_1.2.2          
 [37] maps_3.4.1                  BSgenome_1.67.1            
 [39] susieR_0.12.27              readxl_1.4.1               
 [41] pals_1.7                    rstudioapi_0.14            
 [43] RSQLite_2.2.18              httpcode_0.3.0             
 [45] generics_0.1.3              BiocIO_1.9.0               
 [47] echoconda_0.99.8            dplyr_1.0.10               
 [49] zip_2.2.2                   interp_1.1-3               
 [51] fansi_1.0.3                 DescTools_0.99.47          
 [53] S4Vectors_0.37.0            catalogueR_1.0.0           
 [55] R.methodsS3_1.8.2           lifecycle_1.0.3            
 [57] yaml_2.3.6                  SummarizedExperiment_1.29.1
 [59] BiocFileCache_2.7.0         echoplot_0.99.6            
 [61] grid_4.3.0                  blob_1.2.3                 
 [63] promises_1.2.0.1            crayon_1.5.2               
 [65] dir.expiry_1.7.0            miniUI_0.1.1.1             
 [67] lattice_0.20-45             GenomicFeatures_1.51.2     
 [69] mapproj_1.2.9               KEGGREST_1.39.0            
 [71] MungeSumstats_1.7.1         pillar_1.8.1               
 [73] knitr_1.40                  GenomicRanges_1.51.1       
 [75] rjson_0.2.21                osfr_0.2.9                 
 [77] boot_1.3-28                 gld_2.6.6                  
 [79] codetools_0.2-18            glue_1.6.2                 
 [81] data.table_1.14.4           remotes_2.4.2              
 [83] coloc_5.1.0.1               vctrs_0.5.0                
 [85] png_0.1-7                   testthat_3.1.5             
 [87] XGR_1.1.8                   cellranger_1.1.0           
 [89] gtable_0.3.1                assertthat_0.2.1           
 [91] cachem_1.0.6                dnet_1.1.7                 
 [93] xfun_0.34                   openxlsx_4.2.5.1           
 [95] mime_0.12                   Rfast_2.0.6                
 [97] gargle_1.2.1                ellipsis_0.3.2             
 [99] nlme_3.1-160                usethis_2.1.6              
[101] bit64_4.0.5                 progress_1.2.2             
[103] filelock_1.0.2              googleAuthR_2.0.0          
[105] GenomeInfoDb_1.35.3         rprojroot_2.0.3            
[107] irlba_2.3.5.1               rpart_4.1.19               
[109] colorspace_2.0-3            BiocGenerics_0.45.0        
[111] DBI_1.1.3                   Hmisc_4.7-1                
[113] nnet_7.3-18                 Exact_3.2                  
[115] tidyselect_1.2.0            processx_3.8.0             
[117] bit_4.0.4                   compiler_4.3.0             
[119] curl_4.3.3                  graph_1.77.0               
[121] htmlTable_2.4.1             expm_0.999-6               
[123] basilisk.utils_1.11.0       xml2_1.3.3                 
[125] desc_1.4.2                  DelayedArray_0.25.0        
[127] rtracklayer_1.59.0          checkmate_2.1.0            
[129] scales_1.2.1                hexbin_1.28.2              
[131] echoLD_0.99.8               RBGL_1.75.0                
[133] callr_3.7.3                 RCircos_1.2.2              
[135] rappdirs_0.3.3              stringr_1.4.1              
[137] supraHex_1.37.0             digest_0.6.30              
[139] piggyback_0.1.4             rmarkdown_2.18             
[141] basilisk_1.11.2             XVector_0.39.0             
[143] htmltools_0.5.3             pkgconfig_2.0.3            
[145] jpeg_0.1-9                  base64enc_0.1-3            
[147] MatrixGenerics_1.11.0       echodata_0.99.16           
[149] ensembldb_2.23.1            dbplyr_2.2.1               
[151] fastmap_1.1.0               rlang_1.0.6                
[153] htmlwidgets_1.5.4           shiny_1.7.3                
[155] farver_2.1.1                echofinemap_0.99.4         
[157] jsonlite_1.8.3              BiocParallel_1.33.0        
[159] R.oo_1.25.0                 VariantAnnotation_1.45.0   
[161] RCurl_1.98-1.9              magrittr_2.0.3             
[163] Formula_1.2-4               GenomeInfoDbData_1.2.9     
[165] ggnetwork_0.5.10            patchwork_1.1.2            
[167] munsell_0.5.0               Rcpp_1.0.9                 
[169] ggnewscale_0.4.8            viridis_0.6.2              
[171] ape_5.6-2                   reticulate_1.26            
[173] RcppZiggurat_0.1.6          stringi_1.7.8              
[175] brio_1.1.3                  rootSolve_1.8.2.3          
[177] zlibbioc_1.45.0             MASS_7.3-58.1              
[179] plyr_1.8.8                  pkgbuild_1.3.1             
[181] parallel_4.3.0              ggrepel_0.9.2              
[183] lmom_2.9                    deldir_1.0-6               
[185] echoannot_0.99.10           Biostrings_2.67.0          
[187] splines_4.3.0               hms_1.1.2                  
[189] ps_1.7.2                    igraph_1.3.5               
[191] reshape2_1.4.4              biomaRt_2.55.0             
[193] stats4_4.3.0                pkgload_1.3.1              
[195] crul_1.3                    XML_3.99-0.12              
[197] evaluate_0.18               latticeExtra_0.6-30        
[199] biovizBase_1.47.0           BiocManager_1.30.19        
[201] tzdb_0.3.0                  httpuv_1.6.6               
[203] tidyr_1.2.1                 purrr_0.3.5                
[205] reshape_0.8.9               ggplot2_3.4.0              
[207] echotabix_0.99.8            xtable_1.8-4               
[209] restfulr_0.0.15             AnnotationFilter_1.23.0    
[211] e1071_1.7-12                downloadR_0.99.5           
[213] roxygen2_7.2.2              later_1.3.0                
[215] ragg_1.2.4                  viridisLite_0.4.1          
[217] class_7.3-20.1              OrganismDbi_1.41.0         
[219] tibble_3.1.8                memoise_2.0.1              
[221] AnnotationDbi_1.61.0        GenomicAlignments_1.35.0   
[223] IRanges_2.33.0              cluster_2.1.4