Error when installing the gsynth from Github

xuyiqing / gsynth

Generalized Synthetic Control Method

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... ✓ 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

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

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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xuyiqing / gsynth

Error when installing the gsynth from Github #59