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moodymudskipper / flow

View and Browse Code Using Flow Diagrams
https://moodymudskipper.github.io/flow/
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Installation problems on Ubuntu (RInternals.h missing) #49

Closed jankowtf closed 3 years ago

jankowtf commented 3 years ago

Hi there!

Just wanted to try out your package, but renv::install("moodymudskipper/flow") came back with the following error on Pop!_OS (based on Ubuntu 20.04 LTS):

renv::install("moodymudskipper/flow")
#> Retrieving 'https://api.github.com/repos/moodymudskipper/flow/tarball/3c3972a1f7a3722e3b7b480d393e81b913806604' ...
#>  OK [file is up to date]
#> Installing flow [0.0.1] ...
#>  FAILED
#> Error installing package 'flow':
#> ================================
#> 
#> Warning in untar2(tarfile, files, list, exdir, restore_times) :
#>   skipping pax global extended headers
#> * installing *source* package ‘flow’ ...
#> ** using staged installation
#> ** libs
#> g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/data/Code/Rappster/Stadtsalat/dds.delivduration/service/renv/library/R-4.0/x86_64-pc-linux-gnu/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-5iUtQS/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
#> g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/data/Code/Rappster/Stadtsalat/dds.delivduration/service/renv/library/R-4.0/x86_64-pc-linux-gnu/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-5iUtQS/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c is_browsing.cpp -o is_browsing.o
#> is_browsing.cpp:3:10: fatal error: RInternals.h: No such file or directory
#>     3 | #include <RInternals.h>
#>       |          ^~~~~~~~~~~~~~
#> compilation terminated.
#> make: *** [/usr/lib/R/etc/Makeconf:176: is_browsing.o] Error 1
#> ERROR: compilation failed for package ‘flow’
#> * removing ‘/home/data/Code/Rappster/Stadtsalat/dds.delivduration/service/renv/staging/2/flow’
#> Error: install of package 'flow' failed

Sys.which("make") gives me:

Sys.which("make")
#>            make 
#> "/usr/bin/make"

Build tools check gives me:

rstudioapi::buildToolsCheck()
# [1] TRUE

Session info

sessionInfo()
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Pop!_OS 20.04 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices datasets  utils     methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] compiler_4.0.2  magrittr_1.5    htmltools_0.5.0 tools_4.0.2    
#>  [5] yaml_2.2.1      stringi_1.4.6   rmarkdown_2.3   highr_0.8      
#>  [9] knitr_1.29      stringr_1.4.0   xfun_0.16       digest_0.6.25  
#> [13] rlang_0.4.7     renv_0.11.0     evaluate_0.14
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.2 (2020-06-22)
#>  os       Pop!_OS 20.04 LTS           
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_US:en                    
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       UTC                         
#>  date     2020-08-31                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package     * version date       lib source        
#>  P assertthat    0.2.1   2019-03-21 [?] CRAN (R 4.0.2)
#>  P cli           2.0.2   2020-02-28 [?] CRAN (R 4.0.2)
#>  P crayon        1.3.4   2017-09-16 [?] CRAN (R 4.0.2)
#>  P digest        0.6.25  2020-02-23 [?] CRAN (R 4.0.2)
#>  P evaluate      0.14    2019-05-28 [?] CRAN (R 4.0.2)
#>  P fansi         0.4.1   2020-01-08 [?] CRAN (R 4.0.2)
#>  P glue          1.4.2   2020-08-27 [?] CRAN (R 4.0.2)
#>  P highr         0.8     2019-03-20 [?] CRAN (R 4.0.2)
#>  P htmltools     0.5.0   2020-06-16 [?] CRAN (R 4.0.2)
#>  P knitr         1.29    2020-06-23 [?] CRAN (R 4.0.2)
#>  P magrittr      1.5     2014-11-22 [?] CRAN (R 4.0.2)
#>  P renv          0.11.0  2020-06-26 [?] CRAN (R 4.0.2)
#>  P rlang         0.4.7   2020-07-09 [?] CRAN (R 4.0.2)
#>  P rmarkdown     2.3     2020-06-18 [?] CRAN (R 4.0.2)
#>  P sessioninfo   1.1.1   2018-11-05 [?] CRAN (R 4.0.2)
#>  P stringi       1.4.6   2020-02-17 [?] CRAN (R 4.0.2)
#>  P stringr       1.4.0   2019-02-10 [?] CRAN (R 4.0.2)
#>  P withr         2.2.0   2020-04-20 [?] CRAN (R 4.0.2)
#>  P xfun          0.16    2020-07-24 [?] CRAN (R 4.0.2)
#>  P yaml          2.2.1   2020-02-01 [?] CRAN (R 4.0.2)
#> 
#> [1] /home/data/Code/Rappster/.../<pkg>/renv/library/R-4.0/x86_64-pc-linux-gnu
#> [2] /tmp/RtmpAgO6WX/renv-system-library
#> [3] /tmp/RtmpQUSTBW/renv-system-library
#> 
#>  P ── Loaded and on-disk path mismatch.

Just noticed this P ── Loaded and on-disk path mismatch. :smirk: So I thought potentially rather a renv issue?

But then I closed out of my renv-based project and ran remotes::install_github("moodymudskipper/flow"), however I still see the same error.

Session info for that is

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.2 (2020-06-22)
#>  os       Pop!_OS 20.04 LTS           
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_US:en                    
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       Europe/Berlin               
#>  date     2020-08-31                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date       lib source        
#>  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.2)
#>  cli           2.0.2   2020-02-28 [1] CRAN (R 4.0.2)
#>  crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.2)
#>  digest        0.6.25  2020-02-23 [1] CRAN (R 4.0.2)
#>  evaluate      0.14    2019-05-28 [1] CRAN (R 4.0.2)
#>  fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.2)
#>  glue          1.4.1   2020-05-13 [1] CRAN (R 4.0.2)
#>  highr         0.8     2019-03-20 [1] CRAN (R 4.0.2)
#>  htmltools     0.5.0   2020-06-16 [1] CRAN (R 4.0.2)
#>  knitr         1.29    2020-06-23 [1] CRAN (R 4.0.2)
#>  magrittr      1.5     2014-11-22 [1] CRAN (R 4.0.2)
#>  rlang         0.4.7   2020-07-09 [1] CRAN (R 4.0.2)
#>  rmarkdown     2.3     2020-06-18 [1] CRAN (R 4.0.2)
#>  sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.2)
#>  stringi       1.4.6   2020-02-17 [1] CRAN (R 4.0.2)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.0.2)
#>  withr         2.2.0   2020-04-20 [1] CRAN (R 4.0.2)
#>  xfun          0.16    2020-07-24 [1] CRAN (R 4.0.2)
#>  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.0.2)
#> 
#> [1] /home/janko/R/x86_64-pc-linux-gnu-library/4.0
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
moodymudskipper commented 3 years ago

Hi rappster, thanks for your report, for some reason I had missed it, sorry for that, but I have been solving a related issue, so can you check if it works now ?

jankowtf commented 3 years ago

@moodymudskipper Thanks for looking into this! Just checked it and now everything works like a charm :-) Thanks a lot

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