Installation problem

[miguelft96]

Hi,

I have ran into some issues installing VoxHunt. It seems there is a problem with the Description file. Or am I doing something wrong?

devtools::install_github('quadbiolab/voxhunt')
Downloading GitHub repo quadbiolab/voxhunt@HEAD
✓  checking for file ‘/private/var/folders/4h/h11_g5pj4hz53jwk_gklsky00000gn/T/Rtmp24OLDH/remotes2e4683cbc03/quadbiolab-VoxHunt-b0a9262/DESCRIPTION’ ...
─  preparing ‘voxhunt’:
E  checking DESCRIPTION meta-information ...
   Authors@R field gives no person with maintainer role, valid email
   address and non-empty name.

   See section 'The DESCRIPTION file' in the 'Writing R Extensions'
   manual.

Error: Failed to install 'voxhunt' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr:
E> * checking for file ‘/private/var/folders/4h/h11_g5pj4hz53jwk_gklsky00000gn/T/Rtmp24OLDH/remotes2e4683cbc03/quadbiolab-VoxHunt-b0a9262/DESCRIPTION’ ... OK
E> * preparing ‘voxhunt’:
E> * checking DESCRIPTION meta-information ... ERROR
E> Authors@R field gives no person with maintainer role, valid email
E> address and non-empty name.
E> 
E> See section 'The DESCRIPTION file' in the 'Writing R Extensions'
E> manual.
E> 

Here's my session info, by the way.

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13   magrittr_2.0.1    usethis_2.0.0     devtools_2.3.2    pkgload_1.1.0     R6_2.5.0         
 [7] rlang_0.4.9       fansi_0.4.1       tools_3.6.3       pkgbuild_1.2.0    sessioninfo_1.1.1 cli_2.2.0        
[13] withr_2.3.0       ellipsis_0.3.1    remotes_2.2.0     assertthat_0.2.1  digest_0.6.27     rprojroot_2.0.2  
[19] lifecycle_0.2.0   crayon_1.3.4      processx_3.4.5    purrr_0.3.4       callr_3.5.1       fs_1.5.0         
[25] ps_1.5.0          curl_4.3          testthat_3.0.1    memoise_1.1.0     glue_1.4.2        compiler_3.6.3   
[31] desc_1.2.0        prettyunits_1.1.1

When I updated R to version 4.0.3 I get this error:

devtools::install_github('quadbiolab/voxhunt')
Downloading GitHub repo quadbiolab/voxhunt@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/quadbiolab/voxhunt/tarball/HEAD' failed

Any idea what's causing this? Thank you

[joschif]

Hi miguelft96, there seems to have been a problem with the DESCRIPTION file in the most recent version. I just pushed a new version with the fix, should work better now. Let me know how it goes. Best, Jonas

[joschif]

Also, I have not tested the package in R version 4.0 yet, so I would recommend installing in 3.6. I'll update the package to 4.0 as soon as possible.

[miguelft96]

Hey Jonas, It works perfectly on R 3.6.3 now. Thank you very much! For R 4.0.3 I still get an error message, unfortunately. Thank you for your help and for developing such a nice package!! Best, Miguel

[quadbiolab]

Hi Miguel, In case you are interested, I just pushed a new version of VoxHunt (0.9.0), which should work with R 4.0.3. I'll continue working on it in the next couple of days but feel free to try it. I'll close this for now. Best, Jonas

[RhalenaThomas]

Hello, I'd really like to try out VoxHunt on my scRNAseq from organoids. But I'm having the same install problem as Miguel. I am using R version 4.1.0

Here is my error:

devtools::install_github('quadbiolab/voxhunt') Downloading GitHub repo quadbiolab/voxhunt@HEAD Error in utils::download.file(url, path, method = method, quiet = quiet, : download from 'https://api.github.com/repos/quadbiolab/voxhunt/tarball/HEAD' failed

Here is the session info:

sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

loaded via a namespace (and not attached): [1] Seurat_4.0.0 Rtsne_0.15 colorspace_2.0-0 deldir_0.2-10
[5] ellipsis_0.3.2 ggridges_0.5.3 rprojroot_2.0.2 fs_1.5.0
[9] rstudioapi_0.13 spatstat.data_2.0-0 leiden_0.3.7 listenv_0.8.0
[13] remotes_2.2.0 ggrepel_0.9.1 fansi_0.4.2 codetools_0.2-18
[17] splines_4.1.0 cachem_1.0.4 knitr_1.31 polyclip_1.10-0
[21] pkgload_1.1.0 jsonlite_1.7.2 ica_1.0-2 cluster_2.1.1
[25] png_0.1-7 uwot_0.1.10 shiny_1.6.0 sctransform_0.3.2

Thank you for any help you can provide.

[joschif]

Hi @RhalenaThomas, from your message it's a bit hard for me to tell why exactly the download failed. You can also try to clone the repo with git clone https://github.com/quadbiolab/VoxHunt.git and then install from the local directory with devtools::install_local().