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GESIS-Methods-Hub / andrew

Content Aggregation System for tutorials and vignette of reproducible computational methods.
https://gesis-methods-hub.github.io/andrew/
MIT License
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Fail to build Docker image because dataframe is empty #216

Closed rgaiacs closed 4 months ago

rgaiacs commented 4 months ago

@juliandehne I have the impression that this could be because of R packages version. The R packages are not installed with conda.

The information from my machine:

> devtools::load_all()
ℹ Loading andrew
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS/LAPACK: /home/raniere/micromamba/envs/andrew/lib/libopenblasp-r0.3.27.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] andrew_2.0.0     testthat_3.2.1.1

loaded via a namespace (and not attached):
 [1] tidyr_1.3.1       utf8_1.2.4        generics_0.1.3    stringi_1.8.4    
 [5] hms_1.1.3         digest_0.6.35     magrittr_2.0.3    pkgload_1.3.4    
 [9] fastmap_1.2.0     rprojroot_2.0.4   jsonlite_1.8.8    pkgbuild_1.4.4   
[13] sessioninfo_1.2.2 brio_1.1.5        urlchecker_1.0.1  promises_1.3.0   
[17] purrr_1.0.2       fansi_1.0.6       cli_3.6.2         shiny_1.8.1.1    
[21] rlang_1.1.3       ellipsis_0.3.2    remotes_2.5.0     withr_3.0.0      
[25] cachem_1.0.8      devtools_2.4.5    tools_4.3.3       tzdb_0.4.0       
[29] memoise_2.0.1     dplyr_1.1.4       httpuv_1.6.15     vctrs_0.6.5      
[33] logger_0.3.0      R6_2.5.1          mime_0.12         lifecycle_1.0.4  
[37] git2r_0.33.0      stringr_1.5.1     fs_1.6.4          htmlwidgets_1.6.4
[41] usethis_2.2.3     miniUI_0.1.1.1    pkgconfig_2.0.3   desc_1.4.3       
[45] pillar_1.9.0      later_1.3.2       glue_1.7.0        profvis_0.3.8    
[49] Rcpp_1.0.12       xfun_0.44         tibble_3.2.1      tidyselect_1.2.1 
[53] rstudioapi_0.16.0 knitr_1.46        xtable_1.8-4      htmltools_0.5.8.1
[57] readr_2.1.5       compiler_4.3.3
rgaiacs commented 4 months ago

@juliandehne I believe that we resolved this.

andrew source code uses Conda for isolation. All the dependencies are listed at https://github.com/GESIS-Methods-Hub/andrew/blob/main/env.yaml and installed from there. Note that only part of TidyVerse is installed.

When we run andrew from the conda environment on GNU/Linux (or WSL), it worked. Our hypothesis now is that calling the R system will make the docker call be processed on cmd instead of bash and the output is not processed properly.