fgcz / bfabricShiny

Manage life sciences data using R and b-fabric - a WSDL/REST interface and a tool box; main focus on MS data
http://fgcz-bfabric.uzh.ch
GNU General Public License v3.0
8 stars 1 forks source link

install from Git repo fails #30

Closed tobiasko closed 4 years ago

tobiasko commented 4 years ago
> install_github("cpanse/bfabricShiny", build_vignettes = FALSE, quiet = FALSE)
Downloading GitHub repo cpanse/bfabricShiny@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                             
2: CRAN packages only              
3: None                            
4: rlang  (0.4.7  -> 0.4.8 ) [CRAN]
5: R6     (2.4.1  -> 2.5.0 ) [CRAN]
6: digest (0.6.25 -> 0.6.27) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
Installing 1 packages: PKI
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/PKI_0.1-7.tgz'
Content type 'application/x-gzip' length 1644753 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

The downloaded binary packages are in
    /var/folders/j_/4fgphvp14tlf9ms5jgs503qh0000gn/T//RtmpgVKwgm/downloaded_packages
✓  checking for file ‘/private/var/folders/j_/4fgphvp14tlf9ms5jgs503qh0000gn/T/RtmpgVKwgm/remotes165fe60ba4222/fgcz-bfabricShiny-2db98f3/DESCRIPTION’ ...
─  preparing ‘bfabricShiny’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘bfabricShiny_0.10.14.tar.gz’

* installing *source* package ‘bfabricShiny’ ...
** using staged installation
** R
Error in parse(outFile) : 
  /private/var/folders/j_/4fgphvp14tlf9ms5jgs503qh0000gn/T/Rtmp430YOV/R.INSTALL1736b54d9b835/bfabricShiny/R/ms_queue.R:992:17: unexpected symbol
991:                 host = ipadress #"130.60.81.134",
992:                 port
                     ^
ERROR: unable to collate and parse R files for package ‘bfabricShiny’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/bfabricShiny’
Error: Failed to install 'bfabricShiny' from GitHub:
  (converted from warning) installation of package ‘/var/folders/j_/4fgphvp14tlf9ms5jgs503qh0000gn/T//RtmpgVKwgm/file165fe71b56554/bfabricShiny_0.10.14.tar.gz’ had non-zero exit status
>

Is there a bf10 release available that works on MacOS? Do I need additional libs?

session info

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] devtools_2.3.2 usethis_1.6.3  sloop_1.0.1    rawR_0.0.1    

loaded via a namespace (and not attached):
 [1] rstudioapi_0.11   magrittr_1.5      knitr_1.30        pkgload_1.1.0     R6_2.4.1         
 [6] rlang_0.4.7       fansi_0.4.1       tools_4.0.2       pkgbuild_1.1.0    xfun_0.18        
[11] sessioninfo_1.1.1 cli_2.0.2         withr_2.3.0       remotes_2.2.0     htmltools_0.5.0  
[16] ellipsis_0.3.1    rprojroot_1.3-2   yaml_2.2.1        assertthat_0.2.1  digest_0.6.25    
[21] crayon_1.3.4      processx_3.4.4    callr_3.4.4       fs_1.5.0          ps_1.3.4         
[26] curl_4.3          testthat_2.3.2    memoise_1.1.0     glue_1.4.2        evaluate_0.14    
[31] rmarkdown_2.4     compiler_4.0.2    backports_1.1.10  desc_1.2.0        prettyunits_1.1.1
>
wolski commented 4 years ago

Just pushed a change which fixes the install error. Tested on my machine.