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jrs95 / hyprcoloc

Hypothesis Prioritisation in multi-trait Colocalization
https://jrs95.github.io/hyprcoloc/
GNU General Public License v3.0
46 stars 12 forks source link

Installation error #7

Closed swvanderlaan closed 4 years ago

swvanderlaan commented 4 years ago

Hi,

I am getting the following error. Is there a fix for this?

Thanks

Sander

$ r

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin19.3.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(devtools)
Loading required package: usethis
> install_github("jrs95/hyprcoloc", build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE)
Downloading GitHub repo jrs95/hyprcoloc@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All
2: CRAN packages only
3: None
4: Rcpp (1.0.3 -> 1.0.4) [CRAN]
5: glue (1.3.1 -> 1.3.2) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
1
Rcpp (1.0.3 -> 1.0.4) [CRAN]
glue (1.3.1 -> 1.3.2) [CRAN]
Installing 2 packages: Rcpp, glue
Installing packages into ‘/usr/local/lib/R/3.6/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.4.tar.gz'
Content type 'application/x-gzip' length 2750216 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

trying URL 'https://cloud.r-project.org/src/contrib/glue_1.3.2.tar.gz'
Content type 'application/x-gzip' length 97667 bytes (95 KB)
==================================================
downloaded 95 KB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c api.cpp -o api.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c attributes.cpp -o attributes.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c barrier.cpp -o barrier.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c date.cpp -o date.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c module.cpp -o module.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c rcpp_init.cpp -o rcpp_init.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/Cellar/r/3.6.3_1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/usr/local/Cellar/r/3.6.3_1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /usr/local/lib/R/3.6/site-library/00LOCK-Rcpp/00new/Rcpp/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rcpp)
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c glue.c -o glue.o
clang -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c init.c -o init.o
clang -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c trim.c -o trim.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/3.6.3_1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o glue.so glue.o init.o trim.o -L/usr/local/Cellar/r/3.6.3_1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /usr/local/lib/R/3.6/site-library/00LOCK-glue/00new/glue/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (glue)

The downloaded source packages are in
    ‘/private/var/folders/kc/c5rw4cb94c1c149gsm2ygfc00000gn/T/RtmprHsO6r/downloaded_packages’
✔  checking for file ‘/private/var/folders/kc/c5rw4cb94c1c149gsm2ygfc00000gn/T/RtmprHsO6r/remotes1125e2078f58a/jrs95-hyprcoloc-bdf0021/DESCRIPTION’ ...
─  preparing ‘hyprcoloc’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes
E  creating vignettes (1m 0.8s)
   --- re-building ‘hyprcoloc.Rmd’ using rmarkdown
   Quitting from lines 232-237 (hyprcoloc.Rmd)
   Error: processing vignette 'hyprcoloc.Rmd' failed with diagnostics:
   n != length(v)
   --- failed re-building ‘hyprcoloc.Rmd’

   SUMMARY: processing the following file failed:
     ‘hyprcoloc.Rmd’

   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'hyprcoloc' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> Quitting from lines 232-237 (hyprcoloc.Rmd)
E> Error: processing vignette 'hyprcoloc.Rmd' failed with diagnostics:
E> n != length(v)
E> --- failed re-building ‘hyprcoloc.Rmd’
E>
E> SUMMARY: processing the following file failed:
E>   ‘hyprcoloc.Rmd’
E>
E> Error: Vignette re-building failed.
E> Execution halted
swvanderlaan commented 4 years ago

Also tried this:

$ r

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin19.3.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages("remotes")
Installing package into ‘/usr/local/lib/R/3.6/site-library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors

 1: 0-Cloud [https]                   2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]   4: Australia (Melbourne 2) [https]
 5: Australia (Perth) [https]         6: Austria [https]
 7: Belgium (Ghent) [https]           8: Brazil (BA) [https]
 9: Brazil (PR) [https]              10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]            12: Brazil (SP 2) [https]
13: Bulgaria [https]                 14: China (Hong Kong) [https]
15: China (Guangzhou) [https]        16: China (Lanzhou) [https]
17: China (Shanghai) [https]         18: Costa Rica [https]
19: Denmark [https]                  20: East Asia [https]
21: Ecuador (Cuenca) [https]         22: Ecuador (Quito) [https]
23: France (Lyon 1) [https]          24: France (Lyon 2) [https]
25: France (Marseille) [https]       26: Germany (Erlangen) [https]
27: Germany (Münster) [https]        28: Germany (Regensburg) [https]
29: Greece [https]                   30: Hungary [https]
31: Iceland [https]                  32: Indonesia (Jakarta) [https]
33: Italy (Padua) [https]            34: Japan (Tokyo) [https]
35: Korea (Gyeongsan-si) [https]     36: Korea (Seoul 1) [https]
37: Korea (Ulsan) [https]            38: Mexico (Mexico City) [https]
39: Morocco [https]                  40: Norway [https]
41: Philippines [https]              42: Russia [https]
43: Spain (A Coruña) [https]         44: Sweden [https]
45: Switzerland [https]              46: Taiwan (Taipei) [https]
47: Turkey (Mersin) [https]          48: UK (Bristol) [https]
49: UK (London 1) [https]            50: USA (IA) [https]
51: USA (KS) [https]                 52: USA (MI 1) [https]
53: USA (MI 2) [https]               54: USA (OH) [https]
55: USA (OR) [https]                 56: USA (TN) [https]
57: USA (TX 1) [https]               58: Uruguay [https]
59: (other mirrors)

Selection: 1
Enter an item from the menu, or 0 to exit
Selection: 1
trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.1.1.tar.gz'
Content type 'application/x-gzip' length 134042 bytes (130 KB)
==================================================
downloaded 130 KB

* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)

The downloaded source packages are in
    ‘/private/var/folders/kc/c5rw4cb94c1c149gsm2ygfc00000gn/T/RtmpcvT2bX/downloaded_packages’
> remotes::install_github("jrs95/hyprcoloc")
Skipping install of 'hyprcoloc' from a github remote, the SHA1 (bdf00211) has not changed since last install.
  Use `force = TRUE` to force installation
> remotes::install_github("jrs95/hyprcoloc", force = TRUE)
Downloading GitHub repo jrs95/hyprcoloc@master
✔  checking for file ‘/private/var/folders/kc/c5rw4cb94c1c149gsm2ygfc00000gn/T/RtmpcvT2bX/remotes116ab7a79465a/jrs95-hyprcoloc-bdf0021/DESCRIPTION’ ...
─  preparing ‘hyprcoloc’:
✔  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 ‘hyprcoloc_1.0.tar.gz’

Installing package into ‘/usr/local/lib/R/3.6/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘hyprcoloc’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I"/usr/local/lib/R/3.6/site-library/RcppEigen/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Core:535:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/CholmodSupport:45:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from RcppExports.cpp:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I"/usr/local/lib/R/3.6/site-library/RcppEigen/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c align1.cpp -o align1.o
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Core:535:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/CholmodSupport:45:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I"/usr/local/lib/R/3.6/site-library/RcppEigen/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c align12.cpp -o align12.o
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Core:535:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/CholmodSupport:45:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align12.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I"/usr/local/lib/R/3.6/site-library/RcppEigen/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c align1ind.cpp -o align1ind.o
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Core:535:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/CholmodSupport:45:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I"/usr/local/lib/R/3.6/site-library/RcppEigen/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c align2.cpp -o align2.o
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Core:535:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/CholmodSupport:45:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from align2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I"/usr/local/lib/R/3.6/site-library/RcppEigen/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c regional1.cpp -o regional1.o
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Core:535:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/CholmodSupport:45:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I"/usr/local/lib/R/3.6/site-library/RcppEigen/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c regional1ind.cpp -o regional1ind.o
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Core:535:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/CholmodSupport:45:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional1ind.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/3.6.3_1/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.6/site-library/Rcpp/include" -I"/usr/local/lib/R/3.6/site-library/RcppEigen/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include  -fPIC  -g -O2  -c regional2.cpp -o regional2.o
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:1:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Core:535:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:2:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/LU:47:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Jacobi:29:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Cholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:4:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/QR:17:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Householder:27:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:5:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SVD:48:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:6:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Geometry:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Dense:7:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Eigenvalues:58:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:26:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCore:66:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:27:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/OrderingMethods:71:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:29:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseCholesky:43:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/SparseQR:35:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/Sparse:33:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/CholmodSupport:45:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from regional2.cpp:3:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigen.h:25:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/usr/local/lib/R/3.6/site-library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
17 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -L/usr/local/Cellar/r/3.6.3_1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o hyprcoloc.so RcppExports.o align1.o align12.o align1ind.o align2.o regional1.o regional1ind.o regional2.o -L/usr/local/Cellar/r/3.6.3_1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /usr/local/lib/R/3.6/site-library/00LOCK-hyprcoloc/00new/hyprcoloc/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Rmpfr::.__C__atomicVector’ by ‘Matrix::.__C__atomicVector’ when loading ‘hyprcoloc’
Warning: replacing previous import ‘Rmpfr::tcrossprod’ by ‘Matrix::tcrossprod’ when loading ‘hyprcoloc’
Warning: replacing previous import ‘Rmpfr::crossprod’ by ‘Matrix::crossprod’ when loading ‘hyprcoloc’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Rmpfr::.__C__atomicVector’ by ‘Matrix::.__C__atomicVector’ when loading ‘hyprcoloc’
Warning: replacing previous import ‘Rmpfr::tcrossprod’ by ‘Matrix::tcrossprod’ when loading ‘hyprcoloc’
Warning: replacing previous import ‘Rmpfr::crossprod’ by ‘Matrix::crossprod’ when loading ‘hyprcoloc’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Rmpfr::.__C__atomicVector’ by ‘Matrix::.__C__atomicVector’ when loading ‘hyprcoloc’
Warning: replacing previous import ‘Rmpfr::tcrossprod’ by ‘Matrix::tcrossprod’ when loading ‘hyprcoloc’
Warning: replacing previous import ‘Rmpfr::crossprod’ by ‘Matrix::crossprod’ when loading ‘hyprcoloc’
** testing if installed package keeps a record of temporary installation path
* DONE (hyprcoloc)
> browseVignettes(hyprcoloc)
Error in tools::getVignetteInfo(package, lib.loc, all) :
  object 'hyprcoloc' not found
> library(hyprcoloc)
Warning messages:
1: replacing previous import ‘Rmpfr::.__C__atomicVector’ by ‘Matrix::.__C__atomicVector’ when loading ‘hyprcoloc’
2: replacing previous import ‘Rmpfr::tcrossprod’ by ‘Matrix::tcrossprod’ when loading ‘hyprcoloc’
3: replacing previous import ‘Rmpfr::crossprod’ by ‘Matrix::crossprod’ when loading ‘hyprcoloc’
> browseVignettes(hyprcoloc)
Error in match(x, table, nomatch = 0L) :
  'match' requires vector arguments
jrs95 commented 4 years ago

Hi Sander,

Thanks for letting us know about this issue. It appears that the issue is something to do with an update to one of the package dependencies. We will try and fix it.

If you install the package without the vignette the package should work, as the issue is related to one of the plotting tools.

Best wishes,

James

jrs95 commented 4 years ago

@cnfoley the above issue appears to relate to the iterpc package and the snp.combin function in the sensitivity plot. Could you check out what has changed?

Full error below: Error in self$getnext(-1L, layout, drop = FALSE) : n != length(v) Calls: ... snp.combin -> getall -> -> -> .Call Execution halted

jrs95 commented 4 years ago

@cnfoley I think I have fixed the bug in sensitivity.plot, could you check the history to see what I have done is correct?

swvanderlaan commented 3 years ago

Hi,

I still have an issue with installation - see below the output. It seems it has to do with markdown but this is installed... So I am not quite sure where to start in fixing this. Any suggestions?

Thanks!

Sander

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: aarch64-apple-darwin20.4.0 (64-bit)
Running under: macOS Big Sur 11.3

Matrix products: default
BLAS:   /opt/homebrew/Cellar/openblas/0.3.15_1/lib/libopenblasp-r0.3.15.dylib
LAPACK: /opt/homebrew/Cellar/r/4.1.0/lib/R/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

other attached packages:
[1] markdown_1.1   devtools_2.4.1 usethis_2.0.1

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13   magrittr_2.0.1    pkgload_1.2.1     R6_2.5.0
 [5] rlang_0.4.11      fastmap_1.1.0     tools_4.1.0       pkgbuild_1.2.0
 [9] sessioninfo_1.1.1 cli_2.5.0         withr_2.4.2       ellipsis_0.3.2
[13] remotes_2.3.0     rprojroot_2.0.2   lifecycle_1.0.0   crayon_1.4.1
[17] processx_3.5.2    purrr_0.3.4       callr_3.7.0       fs_1.5.0
[21] ps_1.6.0          curl_4.3.1        testthat_3.0.2    memoise_2.0.0
[25] glue_1.4.2        cachem_1.0.5      compiler_4.1.0    desc_1.3.0
[29] prettyunits_1.1.1
> library(devtools)
install_github("jrs95/hyprcoloc", build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE)
Downloading GitHub repo jrs95/hyprcoloc@HEAD

      File /var/folders/y3/46z02d352fq9jjzq_5jjt1vh0000gn/T//RtmphDwKxG/callr-uev-13c1758ee5370 contains invalid line(s)
         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
      They were ignored

✔  checking for file ‘/private/var/folders/y3/46z02d352fq9jjzq_5jjt1vh0000gn/T/RtmphDwKxG/remotes13c171176c595/jrs95-hyprcoloc-2d80b19/DESCRIPTION’ ...
─  preparing ‘hyprcoloc’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  installing the package to build vignettes
E  creating vignettes (40.1s)
   --- re-building ‘hyprcoloc.Rmd’ using rmarkdown
   Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
   Error: processing vignette 'hyprcoloc.Rmd' failed with diagnostics:
   The 'markdown' package should be installed and declared as a dependency of the 'hyprcoloc' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'markdown' package. Please see https://github.com/yihui/knitr/issues/1864 for more information.
   --- failed re-building ‘hyprcoloc.Rmd’

   SUMMARY: processing the following file failed:
     ‘hyprcoloc.Rmd’

   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'hyprcoloc' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E>   Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
E> Error: processing vignette 'hyprcoloc.Rmd' failed with diagnostics:
E> The 'markdown' package should be installed and declared as a dependency of the 'hyprcoloc' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'markdown' package. Please see https://github.com/yihui/knitr/issues/1864 for more information.
E> --- failed re-building ‘hyprcoloc.Rmd’
E>
E> SUMMARY: processing the following file failed:
E>   ‘hyprcoloc.Rmd’
E>
E> Error: Vignette re-building failed.
E> Execution halted
jrs95 commented 3 years ago

Hi Sander,

Apologies for the delayed response.

This issue is being caused by markdown when creating the vignette. Either install the latest version of markdown using install.packages("markdown") or install the package without compiling the vignette using install_github("jrs95/hyprcoloc”).

Best wishes,

James

On 1 Jun 2021, at 10:28, Sander W. van der Laan @.***> wrote:

Hi,

I still have an issue with installation - see below the output. It seems it has to do with markdown but this is installed... So I am not quite sure where to start in fixing this. Any suggestions?

Thanks!

Sander

sessionInfo() R version 4.1.0 (2021-05-18) Platform: aarch64-apple-darwin20.4.0 (64-bit) Running under: macOS Big Sur 11.3

Matrix products: default BLAS: /opt/homebrew/Cellar/openblas/0.3.15_1/lib/libopenblasp-r0.3.15.dylib LAPACK: /opt/homebrew/Cellar/r/4.1.0/lib/R/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

other attached packages: [1] markdown_1.1 devtools_2.4.1 usethis_2.0.1

loaded via a namespace (and not attached): [1] rstudioapi_0.13 magrittr_2.0.1 pkgload_1.2.1 R6_2.5.0 [5] rlang_0.4.11 fastmap_1.1.0 tools_4.1.0 pkgbuild_1.2.0 [9] sessioninfo_1.1.1 cli_2.5.0 withr_2.4.2 ellipsis_0.3.2 [13] remotes_2.3.0 rprojroot_2.0.2 lifecycle_1.0.0 crayon_1.4.1 [17] processx_3.5.2 purrr_0.3.4 callr_3.7.0 fs_1.5.0 [21] ps_1.6.0 curl_4.3.1 testthat_3.0.2 memoise_2.0.0 [25] glue_1.4.2 cachem_1.0.5 compiler_4.1.0 desc_1.3.0 [29] prettyunits_1.1.1

library(devtools) install_github("jrs95/hyprcoloc", build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE) Downloading GitHub repo jrs95/hyprcoloc@HEAD

  File /var/folders/y3/46z02d352fq9jjzq_5jjt1vh0000gn/T//RtmphDwKxG/callr-uev-13c1758ee5370 contains invalid line(s)
     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
  They were ignored

✔ checking for file ‘/private/var/folders/y3/46z02d352fq9jjzq_5jjt1vh0000gn/T/RtmphDwKxG/remotes13c171176c595/jrs95-hyprcoloc-2d80b19/DESCRIPTION’ ... ─ preparing ‘hyprcoloc’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ installing the package to build vignettes E creating vignettes (40.1s) --- re-building ‘hyprcoloc.Rmd’ using rmarkdown Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1. Error: processing vignette 'hyprcoloc.Rmd' failed with diagnostics: The 'markdown' package should be installed and declared as a dependency of the 'hyprcoloc' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'markdown' package. Please see https://github.com/yihui/knitr/issues/1864 for more information. --- failed re-building ‘hyprcoloc.Rmd’

SUMMARY: processing the following file failed: ‘hyprcoloc.Rmd’

Error: Vignette re-building failed. Execution halted Error: Failed to install 'hyprcoloc' from GitHub: System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines): E> Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1. E> Error: processing vignette 'hyprcoloc.Rmd' failed with diagnostics: E> The 'markdown' package should be installed and declared as a dependency of the 'hyprcoloc' package (e.g., in the 'Suggests' field of DESCRIPTION), because the latter contains vignette(s) built with the 'markdown' package. Please see https://github.com/yihui/knitr/issues/1864 for more information. E> --- failed re-building ‘hyprcoloc.Rmd’ E> E> SUMMARY: processing the following file failed: E> ‘hyprcoloc.Rmd’ E> E> Error: Vignette re-building failed. E> Execution halted — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/jrs95/hyprcoloc/issues/7#issuecomment-851977134, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADLZCQG34IUAC6HATSULJPDTQSR4VANCNFSM4LW2PRFQ.