When trying to install the keras environment in my R studio I get the following error :
> devtools::install_github("rstudio/keras")
Error in library.dynam(lib, package, package.lib) : shared object ‘processx.dylib’ not found - RStudio
I then tried to install the processx package both by using install.packages & manually by downloading it from CRAN, I get :
a) Using install.packages :
trying URL 'http://cran.rstudio.com/src/contrib/processx_3.4.1.tar.gz'
Content type 'application/x-gzip' length 123430 bytes (120 KB)
==================================================
downloaded 120 KB
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/anaconda3=/usr/local/src/conda-prefix -Wall tools/px.c -o tools/px
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
Undefined symbols for architecture x86_64:
"___error", referenced from:
_echo_from_fd in px-c8f109.o
"___stack_chk_fail", referenced from:
_cat2 in px-c8f109.o
_cat in px-c8f109.o
_echo_from_fd in px-c8f109.o
_main in px-c8f109.o
"___stack_chk_guard", referenced from:
_cat2 in px-c8f109.o
_cat in px-c8f109.o
_echo_from_fd in px-c8f109.o
_main in px-c8f109.o
"___stderrp", referenced from:
_usage in px-c8f109.o
_cat2 in px-c8f109.o
_cat in px-c8f109.o
_write_to_fd in px-c8f109.o
_echo_from_fd in px-c8f109.o
_main in px-c8f109.o
"___stdoutp", referenced from:
_echo_from_fd in px-c8f109.o
_main in px-c8f109.o
"_close", referenced from:
_cat in px-c8f109.o
"_exit", referenced from:
_cat2 in px-c8f109.o
_cat in px-c8f109.o
"_fflush", referenced from:
_echo_from_fd in px-c8f109.o
_main in px-c8f109.o
"_fprintf", referenced from:
_cat2 in px-c8f109.o
_cat in px-c8f109.o
_write_to_fd in px-c8f109.o
_echo_from_fd in px-c8f109.o
_main in px-c8f109.o
"_fputs", referenced from:
_main in px-c8f109.o
"_fwrite", referenced from:
_usage in px-c8f109.o
_main in px-c8f109.o
"_getenv", referenced from:
_main in px-c8f109.o
"_open", referenced from:
_cat in px-c8f109.o
"_printf", referenced from:
_main in px-c8f109.o
"_puts", referenced from:
_main in px-c8f109.o
"_read", referenced from:
_cat2 in px-c8f109.o
_cat in px-c8f109.o
_echo_from_fd in px-c8f109.o
"_sleep", referenced from:
_main in px-c8f109.o
"_sscanf", referenced from:
_main in px-c8f109.o
"_strcmp", referenced from:
_cat in px-c8f109.o
_main in px-c8f109.o
"_strerror", referenced from:
_echo_from_fd in px-c8f109.o
"_strlen", referenced from:
_write_to_fd in px-c8f109.o
_echo_from_fd in px-c8f109.o
_main in px-c8f109.o
"_usleep", referenced from:
_main in px-c8f109.o
"_write", referenced from:
_cat2 in px-c8f109.o
_cat in px-c8f109.o
_write_to_fd in px-c8f109.o
_echo_from_fd in px-c8f109.o
_main in px-c8f109.o
(maybe you meant: _write_to_fd)
ld: symbol(s) not found for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Makevars:14: tools/px] Error 1
ERROR: compilation failed for package ‘processx’
* removing ‘/anaconda3/lib/R/library/processx’
* restoring previous ‘/anaconda3/lib/R/library/processx’
Warning in install.packages :
installation of package ‘processx’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/jh/0dcjx7c96kx8sggm0wc_ptfc0000gn/T/RtmpFofLM0/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
b) Installing manually via the Rstudio interface :
After I've loaded it via library(processx) I get the following error :
Error: package or namespace load failed for ‘processx’ in get(Info[i, 1], envir = env):
lazy-load database '/anaconda3/lib/R/library/processx/R/processx.rdb' is corrupt
In addition: Warning message:
In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1
I guess that the whole package processx here is causing me problem... Can someone help?
Here is the version of Rstudio I use :
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /anaconda3/lib/R/lib/libRblas.dylib
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
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] neuralnet_1.44.2 caret_6.0-84 ggplot2_3.2.1 lattice_0.20-38
[5] nnet_7.3-12 InformationValue_1.2.3 NeuralNetTools_1.5.2 reshape_0.8.8
[9] scales_1.0.0 RCurl_1.95-4.12 bitops_1.0-6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 lubridate_1.7.4 tidyr_1.0.0 class_7.3-15 assertthat_0.2.1
[6] zeallot_0.1.0 digest_0.6.22 ipred_0.9-9 foreach_1.4.7 R6_2.4.0
[11] plyr_1.8.4 backports_1.1.5 stats4_3.6.1 evaluate_0.14 pillar_1.4.2
[16] rlang_0.4.1 lazyeval_0.2.2 rstudioapi_0.10 data.table_1.12.6 rpart_4.1-15
[21] Matrix_1.2-17 rmarkdown_1.16 splines_3.6.1 gower_0.2.1 stringr_1.4.0
[26] fastDummies_1.5.0 munsell_0.5.0 compiler_3.6.1 xfun_0.10 pkgconfig_2.0.3
[31] htmltools_0.4.0 tidyselect_0.2.5 tibble_2.1.3 prodlim_2018.04.18 codetools_0.2-16
[36] crayon_1.3.4 dplyr_0.8.3 withr_2.1.2 MASS_7.3-51.4 recipes_0.1.7
[41] ModelMetrics_1.2.2 grid_3.6.1 nlme_3.1-141 gtable_0.3.0 lifecycle_0.1.0
[46] magrittr_1.5 cli_1.1.0 stringi_1.4.3 reshape2_1.4.3 timeDate_3043.102
[51] ellipsis_0.3.0 generics_0.0.2 vctrs_0.2.0 lava_1.6.6 iterators_1.0.12
[56] tools_3.6.1 glue_1.3.1 purrr_0.3.3 rsconnect_0.8.15 survival_2.44-1.1
[61] yaml_2.2.0 colorspace_1.4-1 memoise_1.1.0 knitr_1.25