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"rworkflows_static": incorrect parsing #60

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bschilder opened this issue Jun 17, 2023 · 1 comment
Closed

"rworkflows_static": incorrect parsing #60

bschilder opened this issue Jun 17, 2023 · 1 comment
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@bschilder
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1. Bug description

The "rworkflows_static" yaml written was being incorrectly parsed. This was ultimately due to tiny mistake: adding a single " " at the end of the lines in step 1 of 'actions.yml'.

This caused the "rworkflows_static" files to be written like this:
Screenshot 2023-06-17 at 13 33 58

Removing the extra spaces at the end of each line fixed this:
Screenshot 2023-06-17 at 13 47 18

3. Session info

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 13.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] rworkflows_0.99.10

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0    purrr_1.0.1         colorspace_2.1-0    vctrs_0.6.3        
 [5] generics_0.1.3      htmltools_0.5.5     stats4_4.1.2        yaml_2.3.7         
 [9] utf8_1.2.3          RBGL_1.70.0         XML_3.99-0.14       BiocPkgTools_1.12.2
[13] rlang_1.1.1         pillar_1.9.0        glue_1.6.2          BiocGenerics_0.40.0
[17] RColorBrewer_1.1-3  rvcheck_0.2.1       lifecycle_1.0.3     stringr_1.5.0      
[21] dlstats_0.1.7       munsell_0.5.0       gtable_0.3.3        rvest_1.0.3        
[25] htmlwidgets_1.6.2   biocViews_1.62.1    Biobase_2.54.0      tzdb_0.4.0         
[29] fastmap_1.1.1       RUnit_0.4.32        fansi_1.0.4         readr_2.1.4        
[33] renv_0.17.3         scales_1.2.1        DT_0.28             BiocManager_1.30.21
[37] desc_1.4.2          pkgload_1.3.2       graph_1.72.0        jsonlite_1.8.5     
[41] ggplot2_3.4.2       hms_1.1.3           digest_0.6.31       stringi_1.7.12     
[45] gh_1.4.0            dplyr_1.1.2         grid_4.1.2          rprojroot_2.0.3    
[49] here_1.0.1          cli_3.6.1           tools_4.1.2         bitops_1.0-7       
[53] yulab.utils_0.0.6   magrittr_2.0.3      RCurl_1.98-1.12     tibble_3.2.1       
[57] tidyr_1.3.0         pkgconfig_2.0.3     data.table_1.14.8   xml2_1.3.4         
[61] httr_1.4.6          rstudioapi_0.14     badger_0.2.3        R6_2.5.1           
[65] igraph_1.4.2        compiler_4.1.2     

@bschilder bschilder added the bug Something isn't working label Jun 17, 2023
@bschilder bschilder self-assigned this Jun 17, 2023
@bschilder
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Also added a step to switch "inputs." to "env." when creating the static workflow file:

#### Add action steps to static workflow ####

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