Error when installing the gsynth from Github #59
Comments
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The problem is with C++ complier in Big Sur. Check this out:
http://yiqingxu.org/public/BigSurError.pdf
…On Wed, Apr 14, 2021 at 2:19 PM laresbernardo ***@***.***> wrote:
Hi! I'm trying to install gsynth with
devtools::install_github('xuyiqing/gsynth') but am getting the following
error:
...
✓ checking for file ‘/private/var/folders/hy/8z_f0wrn7qs4pgwqr2l4x4f40000gn/T/RtmpQqfVIf/remotesab377051278e/xuyiqing-gsynth-b6c389b/DESCRIPTION’ ...
─ preparing ‘gsynth’:
✓ 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 ‘gsynth_1.1.8.tar.gz’
* installing *source* package ‘gsynth’ ...
** using staged installation
** libs
/usr/local/Cellar/gcc/8.3.0/bin/g++-8 -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' "-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/local/Cellar/gcc/8.3.0/bin/g++-8 -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' "-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -fPIC -Wall -g -O2 -c interFE.cpp -o interFE.o
interFE.cpp: In function 'Rcpp::List fe_ad_covar_iter(arma::cube, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, int, double)':
interFE.cpp:480:20: warning: comparison of integer expressions of different signedness: 'const uword' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
if (beta0.n_rows == p) {
~~~~~~~~~~~~~^~~~
interFE.cpp: In function 'Rcpp::List fe_ad_inter_covar_iter(arma::cube, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, int, int, int, double, double)':
interFE.cpp:673:20: warning: comparison of integer expressions of different signedness: 'const uword' {aka 'const unsigned int'} and 'int' [-Wsign-compare]
if (beta0.n_rows == p) {
~~~~~~~~~~~~~^~~~
/usr/local/Cellar/gcc/8.3.0/bin/g++-8 -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/Cellar/gcc/8.3.0/lib -o gsynth.so RcppExports.o interFE.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0'
ld: warning: ignoring file /usr/local/gfortran/lib/libgfortran.dylib, building for macOS-x86_64 but attempting to link with file built for unknown-unsupported file format ( 0xFE 0xED 0xFA 0xCE 0x00 0x00 0x00 0x12 0x00 0x00 0x00 0x0A 0x00 0x00 0x00 0x06 )
ld: warning: ignoring file /usr/local/gfortran/lib/libstdc++.dylib, building for macOS-x86_64 but attempting to link with file built for unknown-unsupported file format ( 0xFE 0xED 0xFA 0xCE 0x00 0x00 0x00 0x12 0x00 0x00 0x00 0x0A 0x00 0x00 0x00 0x06 )
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-gsynth/00new/gsynth/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘gsynth’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-gsynth/00new/gsynth/libs/gsynth.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-gsynth/00new/gsynth/libs/gsynth.so, 6): Symbol not found: __ZNSt15basic_streambufIcSt11char_traitsIcEE5imbueERKSt6locale
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-gsynth/00new/gsynth/libs/gsynth.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-gsynth/00new/gsynth/libs/gsynth.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/gsynth’
Error: Failed to install 'gsynth' from GitHub:
(converted from warning) installation of package ‘/var/folders/hy/8z_f0wrn7qs4pgwqr2l4x4f40000gn/T//RtmpQqfVIf/fileab375ffc153d/gsynth_1.1.8.tar.gz’ had non-zero exit status
I've tried in two different computers, same outcome. Sharing 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] pillar_1.5.1 compiler_4.0.3 prettyunits_1.1.1 remotes_2.1.1 tools_4.0.3
[6] testthat_3.0.2 digest_0.6.27 pkgbuild_1.2.0 pkgload_1.1.0 memoise_1.1.0
[11] lifecycle_1.0.0 tibble_3.1.0 pkgconfig_2.0.3 rlang_0.4.10 DBI_1.1.0
[16] cli_2.4.0 rstudioapi_0.13 curl_4.3 yaml_2.2.1 withr_2.4.1
[21] dplyr_1.0.5 fs_1.5.0 generics_0.1.0 desc_1.2.0 vctrs_0.3.7
[26] devtools_2.3.0 rprojroot_2.0.2 tidyselect_1.1.0 glue_1.4.2 R6_2.5.0
[31] processx_3.4.5 fansi_0.4.2 sessioninfo_1.1.1 tidyr_1.1.3 purrr_0.3.4
[36] callr_3.5.1 blob_1.2.1 magrittr_2.0.1 ps_1.5.0 ellipsis_0.3.1
[41] usethis_1.6.1 assertthat_0.2.1 utf8_1.2.1 crayon_1.4.1
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Thanks @xuyiqing that seems to have solved the problem in macOS. So strange and laborious. Thanks! |
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Hi! I'm trying to install
gsynthwithdevtools::install_github('xuyiqing/gsynth')but am getting the following error:I've tried in two different computers, same outcome. Sharing my
sessionInfo():The text was updated successfully, but these errors were encountered: