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RajLabMSSM / echolocatoR

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.
https://rajlabmssm.github.io/echolocatoR
MIT License
30 stars 11 forks source link

vignettes causing errors in GHA (but not locally) #129

Closed bschilder closed 7 months ago

bschilder commented 1 year ago

Might be related to "print" issues: https://github.com/r-lib/actions/issues/319#issuecomment-863992073 https://github.com/r-lib/devtools/issues/2407

bschilder commented 1 year ago

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 commented 1 year ago

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: https://github.com/r-lib/remotes/issues/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 commented 1 year ago

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 commented 1 year ago

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: https://github.com/tidyverse/ggplot2/issues/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 ```