Error installing

[alitinet]

Hi all,

I'm trying to install the package via devtools::install_github("immunogenomics/symphony") but I get the following output:

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

I updated devtools to the latest version and have harmony installed.

Here's my sessionInfo():

R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16

Matrix products: default 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_0.13 magrittr_2.0.1 usethis_2.0.0
[4] devtools_2.3.1.9000 pkgload_1.1.0 R6_2.5.0
[7] rlang_0.4.10 fansi_0.4.1 tools_4.0.3
[10] 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
[16] 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
[22] purrr_0.3.4 callr_3.5.1 fs_1.5.0
[25] ps_1.5.0 curl_4.3 testthat_3.0.1
[28] memoise_1.1.0 glue_1.4.2 compiler_4.0.3
[31] desc_1.2.0 prettyunits_1.1.1

Would appreciate any help!

[joycekang]

Hello,

Sorry you're running into that installation error!

A quick search on your failure message seems to suggest that it may not be specific to Symphony. It may be a Github server issue (https://github.com/dviraran/SingleR/issues/18), or it may be an issue with the particular machine (https://github.com/gadenbuie/xaringanExtra/issues/70). Would you be able to try it again in a few hours or on a different machine and let us know if you're still having the same issue?

Thanks!

[alitinet]

Hey,

I tried again and also on a different device, same issue. As suggested in gadenbuie/xaringanExtra#70 downloading a .zip file and running devtools::install_local at least started the installation but then I got errors when compiling the source code. It seem like it's a specific macOS issue with fortran (solved following privefl/bigstatsr#16 and a very similar issue to RcppCore/RcppArmadillo#262. I haven't figured out how to fix the last one yet but I'll post an update if I will. It's sort of odd because I did install Harmony without any issues.

But anyway, thanks for the links!

[alitinet]

Installing the latest fortran from fxcoudert/gfortran-for-macOS and creating ~/.R/Makevars with the following lines

CXX_STD = CXX11
PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
PKG_CXXFLAGS="-DUSE_FLOAT_TYPES=0"
F77 = gfortran
FC = gfortran
FLIBS = -L/usr/local/gfortran/lib

solved the problem.