ArchR
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can't install ArchR on my mac Sonoma 14.6.1
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
If your issue persists, then please submit this bug report.
PLEASE FILL OUT THE RELEVANT INFORMATION AND DELETE THE UNUSED PORTIONS OF THIS ISSUE TEMPLATE.
trying to install the package results in an error
The downloaded binary packages are in
/var/folders/wf/jh13493j43x_jjyqpzd6396m0000gn/T//RtmpLUbe4G/downloaded_packages
-- R CMD build -------------------------------------------------------------------------------------------------------------------------------------------------------
v checking for file '/private/var/folders/wf/jh13493j43x_jjyqpzd6396m0000gn/T/RtmpLUbe4G/remotes46581186d448/GreenleafLab-ArchR-d9e741c/DESCRIPTION' (555ms)
- preparing 'ArchR': (613ms)
v checking DESCRIPTION meta-information ...
- cleaning src
- checking for LF line-endings in source and make files and shell scripts (992ms)
- checking for empty or unneeded directories
- building 'ArchR_1.0.2.tar.gz'
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
'ArchR/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md'
* installing *source* package 'ArchR' ...
** using staged installation
** libs
using C++ compiler: 'clang version 4.0.0 (tags/RELEASE_400/final)'
using SDK: 'MacOSX14.4.sdk'
/usr/local/clang4/bin/clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Correlation.cpp -o Correlation.o
clang-4.0: warning: optimization flag '-falign-functions=64' is not supported [-Wignored-optimization-argument]
In file included from Correlation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/Rcpp/r/headers.h:66:
In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from /usr/local/clang4/bin/../include/c++/v1/cmath:305:
In file included from /usr/local/clang4/bin/../include/c++/v1/math.h:301:
In file included from /usr/local/include/math.h:32:
In file included from /usr/local/include/Availability.h:177:
/usr/local/include/AvailabilityInternal.h:176:10: fatal error: 'AvailabilityInternalLegacy.h' file not found
#include <AvailabilityInternalLegacy.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [Correlation.o] Error 1
ERROR: compilation failed for package 'ArchR'
* removing '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ArchR'
Warning message:
In i.p(...) :
installation of package '/var/folders/wf/jh13493j43x_jjyqpzd6396m0000gn/T//RtmpLUbe4G/file46585fa196f6/ArchR_1.0.2.tar.gz' had non-zero exit status
any ideas hw to solve this?
thanks
Assa
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] C
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] devtools_2.4.5 usethis_3.0.0
loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 BiocManager_1.30.25 compiler_4.4.1
[4] promises_1.3.0 Rcpp_1.0.13 stringr_1.5.1
[7] callr_3.7.6 later_1.3.2 fastmap_1.2.0
[10] mime_0.12 R6_2.5.1 curl_5.2.2
[13] htmlwidgets_1.6.4 desc_1.4.3 profvis_0.3.8
[16] shiny_1.9.1 rlang_1.1.4 cachem_1.1.0
[19] stringi_1.8.4 httpuv_1.6.15 fs_1.6.4
[22] pkgload_1.4.0 memoise_2.0.1 cli_3.6.3
[25] magrittr_2.0.3 ps_1.7.7 processx_3.8.4
[28] digest_0.6.37 xtable_1.8-4 remotes_2.5.0
[31] lifecycle_1.0.4 vctrs_0.6.5 glue_1.7.0
[34] urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.4
[37] purrr_1.0.2 tools_4.4.1 ellipsis_0.3.2
[40] htmltools_0.5.8.1