Presto installation issues

[StevenJYWu]

I'm having a bit of trouble installing presto. I went to google and couldn't find anything related to the error I got. Any help would be appreiciated!

> devtools::install_github("immunogenomics/presto")
Downloading GitHub repo immunogenomics/presto@HEAD
✓  checking for file ‘/private/var/folders/lf/lzpl1rjx6xz24wv0nph1y1v40000gp/T/RtmpFamSBD/remotes77a33e54cff7/immunogenomics-presto-052085d/DESCRIPTION’ ...
─  preparing ‘presto’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘presto_1.0.0.tar.gz’

* installing *source* package ‘presto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fast_wilcox.cpp -o fast_wilcox.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o presto.so RcppExports.o fast_wilcox.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-presto/00new/presto/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
sh: line 1: 30726 Killed: 9               R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/lf/lzpl1rjx6xz24wv0nph1y1v40000gp/T//Rtmp3kCdkJ/file77ec22d19f5'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/presto’
Error: Failed to install 'presto' from GitHub:
  (converted from warning) installation of package ‘/var/folders/lf/lzpl1rjx6xz24wv0nph1y1v40000gp/T//RtmpFamSBD/file77a34a4849c5/presto_1.0.0.tar.gz’ had non-zero exit status
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4

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     

loaded via a namespace (and not attached):
 [1] rstudioapi_0.11   magrittr_1.5      usethis_1.6.1     devtools_2.3.1    pkgload_1.1.0     R6_2.4.1          rlang_0.4.7       fansi_0.4.1      
 [9] tools_4.0.2       pkgbuild_1.1.0    sessioninfo_1.1.1 cli_2.0.2         withr_2.2.0       ellipsis_0.3.1    remotes_2.2.0     assertthat_0.2.1 
[17] digest_0.6.25     rprojroot_1.3-2   crayon_1.3.4      processx_3.4.3    callr_3.4.3       fs_1.5.0          ps_1.3.4          curl_4.3         
[25] testthat_2.3.2    memoise_1.1.0     glue_1.4.2        compiler_4.0.2    desc_1.2.0        backports_1.1.9   prettyunits_1.1.1

[StevenJYWu]

Duplicate issue. https://github.com/immunogenomics/harmony/issues/90#issuecomment-657058816

[slowkow]

Hi @StevenJYWu, thanks for reporting the issue. If it's possible to share exactly what you did to solve the issue, that might be valuable for developers and also for other users.

Thanks for linking to the duplicate issue, by the way.

[StevenJYWu]

I cloned presto, deleted the data files, and the installed locally. Just like what's happening in harmony maybe the data files might be dependent on some version of R?

[slowkow]

Interesting! Thank you for sharing.

When I get a chance, I'll try to fix this data file issue in harmony and presto.