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Bioconductor / AnVILPublish

https://bioconductor.org/packages/AnVILPublish
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general failure #2

Closed vjcitn closed 4 years ago

vjcitn commented 4 years ago

Nothing is processed or propagated. When I use a novel name I am asked to use update. And then there are api md5sum warnings... A workspace is created but DESCRIPTION does not propagate and no notebooks are made.

use 'update = TRUE' to make changes to the workspace
Warning messages:
1: In citation(package, directory) :
  no date field in DESCRIPTION file of package ‘ontoProc’
2: In citation(package, directory) :
  could not determine year for ‘ontoProc’ from package DESCRIPTION file
> ?as_workspace
> as_workspace("ontoProc", "landmarkanvil2", "testop", create=TRUE)
Warning messages:
1: In .service_validate_md5sum(api_reference_url, api_reference_md5sum) :
  service version differs from validated version
    service url: https://api.firecloud.org/api-docs.yaml
    observed md5sum: 0989f3842507d99b29a5dbed98a57a45
    expected md5sum: ebaeb7e317b1702763a1961242d0666f
2: In citation(package, directory) :
  no date field in DESCRIPTION file of package ‘ontoProc’
3: In citation(package, directory) :
  could not determine year for ‘ontoProc’ from package DESCRIPTION file
> sessionInfo()
R version 4.0.2 Patched (2020-07-19 r78892)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS (fossa-melisa X20)

Matrix products: default
BLAS:   /home/stvjc/R-4-0-dist/lib/R/lib/libRblas.so
LAPACK: /home/stvjc/R-4-0-dist/lib/R/lib/libRlapack.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       

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

other attached packages:
[1] AnVILPublish_0.0.11 rmarkdown_2.3      

loaded via a namespace (and not attached):
 [1] whisker_0.4          knitr_1.29           magrittr_1.5        
 [4] tidyselect_1.1.0     R6_2.4.1             rlang_0.4.7         
 [7] httr_1.4.2           dplyr_1.0.2          tools_4.0.2         
[10] xfun_0.16            lambda.r_1.2.4       futile.logger_1.4.3 
[13] htmltools_0.5.0      ellipsis_0.3.1       yaml_2.2.1          
[16] AnVIL_1.1.14         digest_0.6.25        tibble_3.0.3        
[19] lifecycle_0.2.0      crayon_1.3.4         startup_0.14.1      
[22] BiocManager_1.30.10  purrr_0.3.4          formatR_1.7         
[25] vctrs_0.3.2          futile.options_1.0.1 rapiclient_0.1.3    
[28] curl_4.3             glue_1.4.1           evaluate_0.14       
[31] compiler_4.0.2       pillar_1.4.6         generics_0.0.2      
[34] jsonlite_1.7.0       pkgconfig_2.0.3
mtmorgan commented 4 years ago

Please BiocManager::install("Bioconductor/AnVIL") to get the most recent version of the AnVIL package where the checksum checks do not occur.

If you're updating an existing workspace (ontoProc is an existing workspace) then add update = TRUE

as_workspace("ontoProc", "landmarkanvil2", "testop", update=TRUE)

Can you provide a more careful example? For instance the code snippet starts with output, but no idea of input?

vjcitn commented 4 years ago

Working nicely after the BiocManager install -- I had been working from the current git source.