Issue with Seurat installation in R version 4.0.2

[kmuench]

Hello,

I just upgraded to R v4, and I'm running into some mystery issues while re-installing Seurat. Is Seurat compatible with R v4?

Thank you for your work on this library!

Details:

When I try to reinstall by typing

BiocManager::install("Seurat")

The installation initially proceeds as normal:

installing the source package ‘Seurat’

trying URL 'https://cran.rstudio.com/src/contrib/Seurat_3.2.0.tar.gz'
Content type 'application/x-gzip' length 1482089 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘Seurat’ ...
** package ‘Seurat’ successfully unpacked and MD5 sums checked
** using staged installation

But then I see:

** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ModularityOptimizer.cpp -o ModularityOptimizer.o
ModularityOptimizer.cpp:762:7: warning: unused variable 'n2_max' [-Wunused-variable]
  int n2_max = *std::max_element(node2.cbegin(), node2.cend());
      ^
ModularityOptimizer.cpp:761:7: warning: unused variable 'n1_max' [-Wunused-variable]
  int n1_max = *std::max_element(node1.cbegin(), node1.cend());
      ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RModularityOptimizer.cpp -o RModularityOptimizer.o
In file included from RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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
                             ^

The "pragma" error then prints out ~20 times, then the clang error, then the 20 pragma errors, then that whole cycle repeats 5-6 times until finally the installation ends with:

installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 51412 Done                    echo 'tools:::.install_packages()'
     51413 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
	‘/private/var/folders/n9/_hzybkxd18d3gph5qlqhmsw40000gr/T/RtmpAAMwJ8/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘Seurat’ had non-zero exit status

If I attempt to re-install Seurat, I then get an error recommending I try removing the 00LOCK file.

sessionInfo:

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pheatmap_1.0.12             SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.2 DelayedArray_0.14.1         matrixStats_0.56.0          Biobase_2.48.0              GenomicRanges_1.40.0        GenomeInfoDb_1.24.2        
 [9] IRanges_2.22.2              S4Vectors_0.26.1            BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2     BiocManager_1.30.10    compiler_4.0.2         pillar_1.4.6           XVector_0.28.0         base64enc_0.1-3        bitops_1.0-6           viridis_0.5.1          tools_4.0.2            zlibbioc_1.34.0       
[11] digest_0.6.25          jsonlite_1.7.0         evaluate_0.14          viridisLite_0.3.0      lifecycle_0.2.0        tibble_3.0.3           gtable_0.3.0           lattice_0.20-41        pkgconfig_2.0.3        rlang_0.4.7           
[21] Matrix_1.2-18          rstudioapi_0.11        yaml_2.2.1             xfun_0.15              gridExtra_2.3          GenomeInfoDbData_1.2.3 stringr_1.4.0          dplyr_1.0.0            knitr_1.29             generics_0.0.2        
[31] vctrs_0.3.2            tidyselect_1.1.0       grid_4.0.2             glue_1.4.1             R6_2.4.1               rmarkdown_2.3          purrr_0.3.4            ggplot2_3.3.2          magrittr_1.5           htmltools_0.5.0       
[41] scales_1.1.1           ellipsis_0.3.1         colorspace_1.4-1       stringi_1.4.6          RCurl_1.98-1.2         munsell_0.5.0          crayon_1.3.4          

[mojaveazure]

The prama error is a warning and okay to ignore. The issue is that your R session is killing the installation process

51413 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

Unfortunately, the error that's happening is being swallowed here. Can you try installing Seurat again using R in the terminal instead of RStudio?

[rhondabacher]

This is happening to me as well. Using the terminal doesn't seem to produce a more helpful error:

17 warnings generated.
/usr/local/clang4/bin/clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o Seurat.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o integration.o snn.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 1870 Done echo 'tools:::.install_packages()'
1872 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

[kmuench]

This is happening to me as well. Using the terminal doesn't seem to produce a more helpful error:

17 warnings generated.
/usr/local/clang4/bin/clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o Seurat.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o integration.o snn.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 1870 Done echo 'tools:::.install_packages()'
1872 Killed: 9 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

Agreed, I tried in the R console and got the same error:

installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 72242 Done                    echo 'tools:::.install_packages()'
     72243 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
	‘/private/var/folders/n9/_hzybkxd18d3gph5qlqhmsw40000gr/T/RtmpDANaaI/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘Seurat’ had non-zero exit status

[mojaveazure]

Hmm, it seems as though R is having trouble installing the latest release from source. We've built a binary of Seurat 3.2.0 for macOS under R v4, you can install it with the following:

install.packages("Seurat", repos = c("https://seurat.nygenome.org/", "https://cloud.r-project.org"))

Let me know if this works for you

[kmuench]

Thank you so much!

With the above, I get the following error:

Warning in install.packages :
  unable to access index for repository https://cloud.r-project.org/src/contrib:
  cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES'
Warning in install.packages :
  package ‘Seurat’ is not available (for R version 4.0.2)
Warning in install.packages :
  unable to access index for repository https://cloud.r-project.org/bin/macosx/contrib/4.0:
  cannot open URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/PACKAGES'

Since it looked like it might be looking for the Seurat binary in the wrong place on cloud.r-project.org, I removed the second repo from that flag and then just got the "Seurat is not available for R4.0.2" error

[mojaveazure]

Huh, it's weird that you can't see https://cloud.r-project.org/; looking back through your issue, you were using https://cran.rstudio.com before so you can replace https://cloud.r-project.org/ with https://cran.rstudio.com

As for the second issue, what happens if you run the following in the terminal (not R)

curl https://seurat.nygenome.org/bin/macosx/contrib/4.0/PACKAGES

[rhondabacher]

The download works OK! But then I am unable to load the package. Am I using this incorrectly?

install.packages("Seurat", repos = c("https://seurat.nygenome.org/", "https://cran.rstudio.com"))
trying URL 'https://seurat.nygenome.org/bin/macosx/contrib/4.0/Seurat_3.2.0.tgz'
Content type 'application/octet-stream' length 1976967 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

The downloaded binary packages are in
/var/folders/gc/tf5lysk92375n12zjcl41dh9xl9rpg/T//RtmpbeulfE/downloaded_packages

library(Seurat)
Error: package or namespace load failed for ‘Seurat’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Seurat/libs/Seurat.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Seurat/libs/Seurat.so, 6): Library not loaded: /usr/local/opt/r/lib/R/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Seurat/libs/Seurat.so
Reason: image not found

[kmuench]

The download works OK! But then I am unable to load the package. Am I using this incorrectly?

install.packages("Seurat", repos = c("https://seurat.nygenome.org/", "https://cran.rstudio.com"))
trying URL 'https://seurat.nygenome.org/bin/macosx/contrib/4.0/Seurat_3.2.0.tgz'
Content type 'application/octet-stream' length 1976967 bytes (1.9 MB)

downloaded 1.9 MB

The downloaded binary packages are in
/var/folders/gc/tf5lysk92375n12zjcl41dh9xl9rpg/T//RtmpbeulfE/downloaded_packages

library(Seurat)
Error: package or namespace load failed for ‘Seurat’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Seurat/libs/Seurat.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Seurat/libs/Seurat.so, 6): Library not loaded: /usr/local/opt/r/lib/R/lib/libR.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Seurat/libs/Seurat.so
Reason: image not found

I am getting the same issue (except for I had to do a couple extra steps before I got to the same point:

1. Install gfortran
2. BiocManager::install("deldir") )

[mojaveazure]

That's interesting that neither of you are able to install Seurat. How did you guys install R? Did you download the app from CRAN, did you install it through Conda, or some other method of installation?

[slowkow]

I have exactly the same error, line for line verbatim. I had Seurat installed OK on R 3.6 and now I can't get it installed on R 4.0

install.packages("Seurat")

17 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Seurat.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o integration.o snn.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 63947 Done                    echo 'tools:::.install_packages()'
     63948 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
        ‘/private/var/folders/_p/36jhfrg52ld1643fftf08x740000gp/T/RtmptR3lZo/downloaded_packages’
Warning message:
In install.packages("Seurat") :
  installation of package ‘Seurat’ had non-zero exit status

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] devtools_2.3.0 usethis_1.6.1

loaded via a namespace (and not attached):
 [1] ps_1.3.3           fansi_0.4.1        prettyunits_1.1.1  rprojroot_1.3-2
 [5] withr_2.2.0        digest_0.6.25      crayon_1.3.4       assertthat_0.2.1
 [9] R6_2.4.1           backports_1.1.8    magrittr_1.5       rlang_0.4.7
[13] cli_2.0.2          remotes_2.1.1      fs_1.4.2           testthat_2.3.2
[17] callr_3.4.3        ellipsis_0.3.1     desc_1.2.0         tools_4.0.2
[21] glue_1.4.1         compiler_4.0.2     pkgload_1.1.0      processx_3.4.3
[25] pkgbuild_1.1.0     sessioninfo_1.1.1  memoise_1.1.0.9000

I also recently tried to help others with a similar error with our harmony R package. I still don't fully understand it.

$ cat ~/.R/Makevars # it is empty

$ readlink -f $(which gfortran)
/usr/local/gfortran/bin/gfortran

$ gfortran --version
GNU Fortran (GCC) 6.3.0
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ readlink -f $(which clang++)
/usr/bin/clang++

$ clang++ --version
Apple clang version 11.0.0 (clang-1100.0.33.17)
Target: x86_64-apple-darwin19.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

[slowkow]

I tried installing gfortran 8.2.0 as recommended here. It didn't help.

https://cloud.r-project.org/

$ gfortran --version
GNU Fortran (GCC) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I get a very slightly different error. Now it failed on line 64939 instead of 63947:

installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 64939 Done                    echo 'tools:::.install_packages()'
     64940 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}

The downloaded source packages are in
        ‘/private/var/folders/_p/36jhfrg52ld1643fftf08x740000gp/T/RtmpsGzMza/downloaded_packages’
Warning message:
In install.packages("Seurat") :
  installation of package ‘Seurat’ had non-zero exit status

[slowkow]

I don't know why many of us with macOS are having problems while Travis is reporting success with this system information:

$ Rscript -e 'sessionInfo()'
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6

[slowkow]

I forked Seurat and launched GitHub Actions to test R CMD check with macOS 10.15.5:

https://github.com/slowkow/seurat/runs/884059520?check_suite_focus=true

The check passed without errors.

Since this issue appears in multiple R packages that use Rcpp, my hunch is that those of us experiencing this issue have probably changed the compilers on our local macOS systems, but I don't know exactly what the problem might be.

[slowkow]

Instead of choosing to compile Seurat 3.2.0, I tried choosing the binary version 3.1.5.

Then, running library(Seurat) instantly gives me Killed: 9. Searching Google for this error gives a lot of results and might help folks to investigate this problem. There seem to be a lot of possible causes...

> remove.packages("Seurat")
Removing package from ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
(as ‘lib’ is unspecified)
> install.packages("Seurat")

  There is a binary version available but the source version is later:
       binary source needs_compilation
Seurat  3.1.5  3.2.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no
trying URL 'https://cloud.r-project.org/bin/macosx/contrib/4.0/Seurat_3.1.5.tgz'
Content type 'application/x-gzip' length 3186966 bytes (3.0 MB)
==================================================
downloaded 3.0 MB


The downloaded binary packages are in
        /var/folders/_p/36jhfrg52ld1643fftf08x740000gp/T//Rtmpi0g4ib/downloaded_packages
> library(Seurat)
Killed: 9

After the crash, I can see there is a new entry under Crash Reports in the Console app for macOS.

I think this might be the important bit:

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (Code Signature Invalid)
Exception Codes:       0x0000000000000032, 0x000000010b784000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Reason:    Namespace CODESIGNING, Code 0x2

kernel messages:

VM Regions Near 0x10b784000:
    VM_ALLOCATE            000000010b783000-000000010b784000 [    4K] rwx/rwx SM=PRV  
--> mapped file            000000010b784000-000000010b785000 [    4K] r--/r-x SM=PRV  �
    __TEXT                 000000010b785000-000000010b7ae000 [  164K] r-x/rwx SM=COW  /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib

The full crash report

Process:               R [2660]
Path:                  /Library/Frameworks/R.framework/Versions/4.0/Resources/bin/exec/R
Identifier:            R
Version:               0
Code Type:             X86-64 (Native)
Parent Process:        bash [67484]
Responsible:           iTerm2 [715]
User ID:               502

Date/Time:             2020-07-18 14:32:12.469 -0400
OS Version:            Mac OS X 10.15.5 (19F101)
Report Version:        12
Bridge OS Version:     4.5 (17P5300)
Anonymous UUID:        B4BCD4AE-D5A2-FADA-D9CB-55F8C4B47C43

Sleep/Wake UUID:       4B8044E9-A581-462F-A7DB-EE4272A57794

Time Awake Since Boot: 1700000 seconds
Time Since Wake:       19000 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (Code Signature Invalid)
Exception Codes:       0x0000000000000032, 0x000000010b784000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Reason:    Namespace CODESIGNING, Code 0x2

kernel messages:

VM Regions Near 0x10b784000:
    VM_ALLOCATE            000000010b783000-000000010b784000 [    4K] rwx/rwx SM=PRV  
--> mapped file            000000010b784000-000000010b785000 [    4K] r--/r-x SM=PRV  �
    __TEXT                 000000010b785000-000000010b7ae000 [  164K] r-x/rwx SM=COW  /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib

Application Specific Information:
dyld: in dlopen()
/Users/kamil/miniconda3/lib/libmkl_intel_thread.dylib

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   dyld                          	0x0000000110edf430 bcmp + 208
1   dyld                          	0x0000000110ea65ac ImageLoaderMachO::validateFirstPages(linkedit_data_command const*, int, unsigned char const*, unsigned long, long long, ImageLoader::LinkContext const&) + 104
2   dyld                          	0x0000000110eac446 ImageLoaderMachOCompressed::instantiateFromFile(char const*, int, unsigned char const*, unsigned long, unsigned long long, unsigned long long, stat const&, unsigned int, unsigned int, linkedit_data_command const*, encryption_info_command const*, ImageLoader::LinkContext const&) + 310
3   dyld                          	0x0000000110ea5638 ImageLoaderMachO::instantiateFromFile(char const*, int, unsigned char const*, unsigned long, unsigned long long, unsigned long long, stat const&, ImageLoader::LinkContext const&) + 158
4   dyld                          	0x0000000110e90e23 dyld::loadPhase6(int, stat const&, char const*, dyld::LoadContext const&) + 728
5   dyld                          	0x0000000110e98a7f dyld::loadPhase5(char const*, char const*, dyld::LoadContext const&, unsigned int&, std::__1::vector >*) + 1422
6   dyld                          	0x0000000110e9848f dyld::loadPhase4(char const*, char const*, dyld::LoadContext const&, unsigned int&, std::__1::vector >*) + 185
7   dyld                          	0x0000000110e981f9 dyld::loadPhase3(char const*, char const*, dyld::LoadContext const&, unsigned int&, std::__1::vector >*) + 1435
8   dyld                          	0x0000000110e978b3 dyld::loadPhase1(char const*, char const*, dyld::LoadContext const&, unsigned int&, std::__1::vector >*) + 183
9   dyld                          	0x0000000110e909bb dyld::loadPhase0(char const*, char const*, dyld::LoadContext const&, unsigned int&, std::__1::vector >*) + 487
10  dyld                          	0x0000000110e90578 dyld::load(char const*, dyld::LoadContext const&, unsigned int&) + 185
11  dyld                          	0x0000000110e9cd3d dlopen_internal + 419
12  libdyld.dylib                 	0x00007fff69192d8a dlopen + 171
13  libmkl_rt.dylib               	0x000000010eb04900 mkl_sdl_load_function + 912
14  libmkl_rt.dylib               	0x000000010eb010d9 MKL_Get_Version + 41
15  libpython3.7m.dylib           	0x000000010e7a71d6 _PyMethodDef_RawFastCallKeywords + 790
16  libpython3.7m.dylib           	0x000000010e7a726d _PyCFunction_FastCallKeywords + 45
17  libpython3.7m.dylib           	0x000000010e8af2bb call_function + 603
18  libpython3.7m.dylib           	0x000000010e8a64b5 _PyEval_EvalFrameDefault + 7893
19  libpython3.7m.dylib           	0x000000010e8a414c _PyEval_EvalCodeWithName + 3308
20  libpython3.7m.dylib           	0x000000010e89f985 builtin_exec + 901
21  libpython3.7m.dylib           	0x000000010e7a62ac _PyMethodDef_RawFastCallDict + 652
22  libpython3.7m.dylib           	0x000000010e7a7577 PyCFunction_Call + 87
23  libpython3.7m.dylib           	0x000000010e8a6902 _PyEval_EvalFrameDefault + 8994
24  libpython3.7m.dylib           	0x000000010e8a414c _PyEval_EvalCodeWithName + 3308
25  libpython3.7m.dylib           	0x000000010e7a6ea6 _PyFunction_FastCallKeywords + 230
26  libpython3.7m.dylib           	0x000000010e8af32e call_function + 718
27  libpython3.7m.dylib           	0x000000010e8a64b5 _PyEval_EvalFrameDefault + 7893
28  libpython3.7m.dylib           	0x000000010e7a691e function_code_fastcall + 254
29  libpython3.7m.dylib           	0x000000010e8af32e call_function + 718
30  libpython3.7m.dylib           	0x000000010e8a649b _PyEval_EvalFrameDefault + 7867
31  libpython3.7m.dylib           	0x000000010e7a691e function_code_fastcall + 254
32  libpython3.7m.dylib           	0x000000010e8af32e call_function + 718
33  libpython3.7m.dylib           	0x000000010e8a6546 _PyEval_EvalFrameDefault + 8038
34  libpython3.7m.dylib           	0x000000010e7a691e function_code_fastcall + 254
35  libpython3.7m.dylib           	0x000000010e8af32e call_function + 718
36  libpython3.7m.dylib           	0x000000010e8a6546 _PyEval_EvalFrameDefault + 8038
37  libpython3.7m.dylib           	0x000000010e7a691e function_code_fastcall + 254
38  libpython3.7m.dylib           	0x000000010e7a8908 object_vacall + 392
39  libpython3.7m.dylib           	0x000000010e7a8a3d _PyObject_CallMethodIdObjArgs + 173
40  libpython3.7m.dylib           	0x000000010e8d1c6c PyImport_ImportModuleLevelObject + 2124
41  libpython3.7m.dylib           	0x000000010e89e595 builtin___import__ + 149
42  libpython3.7m.dylib           	0x000000010e7a769c PyCFunction_Call + 380
43  libpython3.7m.dylib           	0x000000010e8a6902 _PyEval_EvalFrameDefault + 8994
44  libpython3.7m.dylib           	0x000000010e8a414c _PyEval_EvalCodeWithName + 3308
45  libpython3.7m.dylib           	0x000000010e7a6ea6 _PyFunction_FastCallKeywords + 230
46  libpython3.7m.dylib           	0x000000010e8af32e call_function + 718
47  libpython3.7m.dylib           	0x000000010e8a6546 _PyEval_EvalFrameDefault + 8038
48  libpython3.7m.dylib           	0x000000010e7a691e function_code_fastcall + 254
49  libpython3.7m.dylib           	0x000000010e8af32e call_function + 718
50  libpython3.7m.dylib           	0x000000010e8a6546 _PyEval_EvalFrameDefault + 8038
51  libpython3.7m.dylib           	0x000000010e7a691e function_code_fastcall + 254
52  libpython3.7m.dylib           	0x000000010e7a8908 object_vacall + 392
53  libpython3.7m.dylib           	0x000000010e7a8a3d _PyObject_CallMethodIdObjArgs + 173
54  libpython3.7m.dylib           	0x000000010e8d1c6c PyImport_ImportModuleLevelObject + 2124
55  libpython3.7m.dylib           	0x000000010e89e595 builtin___import__ + 149
56  libpython3.7m.dylib           	0x000000010e7a769c PyCFunction_Call + 380
57  libpython3.7m.dylib           	0x000000010e8a6902 _PyEval_EvalFrameDefault + 8994
58  libpython3.7m.dylib           	0x000000010e8a414c _PyEval_EvalCodeWithName + 3308
59  libpython3.7m.dylib           	0x000000010e7a6ea6 _PyFunction_FastCallKeywords + 230
60  libpython3.7m.dylib           	0x000000010e8af32e call_function + 718
61  libpython3.7m.dylib           	0x000000010e8a6546 _PyEval_EvalFrameDefault + 8038
62  libpython3.7m.dylib           	0x000000010e7a691e function_code_fastcall + 254
63  libpython3.7m.dylib           	0x000000010e8af32e call_function + 718
64  libpython3.7m.dylib           	0x000000010e8a6546 _PyEval_EvalFrameDefault + 8038
65  libpython3.7m.dylib           	0x000000010e7a691e function_code_fastcall + 254
66  libpython3.7m.dylib           	0x000000010e7a8908 object_vacall + 392
67  libpython3.7m.dylib           	0x000000010e7a8a3d _PyObject_CallMethodIdObjArgs + 173
68  libpython3.7m.dylib           	0x000000010e8d1c6c PyImport_ImportModuleLevelObject + 2124
69  libpython3.7m.dylib           	0x000000010e89e595 builtin___import__ + 149
70  libpython3.7m.dylib           	0x000000010e7a628d _PyMethodDef_RawFastCallDict + 621
71  libpython3.7m.dylib           	0x000000010e7a5c80 _PyObject_FastCallDict + 272
72  libpython3.7m.dylib           	0x000000010e7a7c7a _PyObject_CallFunctionVa + 266
73  libpython3.7m.dylib           	0x000000010e7a7b4b PyObject_CallFunction + 139
74  libpython3.7m.dylib           	0x000000010e8d1237 PyImport_Import + 631
75  libpython3.7m.dylib           	0x000000010e8d27fc PyImport_ImportModule + 28
76  reticulate.so                 	0x000000010e71c2c7 libpython::import_numpy_api(bool, std::__1::basic_string, std::__1::allocator >*) + 39 (libpython.cpp:325)
77  reticulate.so                 	0x000000010e728010 py_initialize(std::__1::basic_string, std::__1::allocator > const&, std::__1::basic_string, std::__1::allocator > const&, std::__1::basic_string, std::__1::allocator > const&, std::__1::basic_string, std::__1::allocator > const&, bool, bool, std::__1::basic_string, std::__1::allocator > const&) + 896 (python.cpp:1710)
78  reticulate.so                 	0x000000010e704e6a _reticulate_py_initialize + 858 (RcppExports.cpp:117)
79  libR.dylib                    	0x000000010b316de7 R_doDotCall + 2679
80  libR.dylib                    	0x000000010b3627fa bcEval + 105338 (eval.c:7655)
81  libR.dylib                    	0x000000010b348541 Rf_eval + 385
82  libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
83  libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
84  libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
85  libR.dylib                    	0x000000010b348541 Rf_eval + 385
86  libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
87  libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
88  libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
89  libR.dylib                    	0x000000010b348541 Rf_eval + 385
90  libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
91  libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
92  libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
93  libR.dylib                    	0x000000010b348541 Rf_eval + 385
94  libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
95  libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
96  libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
97  libR.dylib                    	0x000000010b348541 Rf_eval + 385
98  libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
99  libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
100 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
101 libR.dylib                    	0x000000010b348541 Rf_eval + 385
102 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
103 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
104 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
105 libR.dylib                    	0x000000010b348541 Rf_eval + 385
106 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
107 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
108 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
109 libR.dylib                    	0x000000010b348541 Rf_eval + 385
110 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
111 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
112 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
113 libR.dylib                    	0x000000010b348541 Rf_eval + 385
114 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
115 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
116 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
117 libR.dylib                    	0x000000010b348541 Rf_eval + 385
118 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
119 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
120 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
121 libR.dylib                    	0x000000010b348541 Rf_eval + 385
122 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
123 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
124 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
125 libR.dylib                    	0x000000010b348541 Rf_eval + 385
126 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
127 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
128 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
129 libR.dylib                    	0x000000010b348541 Rf_eval + 385
130 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
131 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
132 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
133 libR.dylib                    	0x000000010b348541 Rf_eval + 385
134 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
135 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
136 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
137 libR.dylib                    	0x000000010b348541 Rf_eval + 385
138 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
139 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
140 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
141 libR.dylib                    	0x000000010b348541 Rf_eval + 385
142 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
143 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
144 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
145 libR.dylib                    	0x000000010b348541 Rf_eval + 385
146 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
147 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
148 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
149 libR.dylib                    	0x000000010b348541 Rf_eval + 385
150 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
151 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
152 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
153 libR.dylib                    	0x000000010b348541 Rf_eval + 385
154 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
155 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
156 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
157 libR.dylib                    	0x000000010b348541 Rf_eval + 385
158 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
159 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
160 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
161 libR.dylib                    	0x000000010b348541 Rf_eval + 385
162 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
163 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
164 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
165 libR.dylib                    	0x000000010b348541 Rf_eval + 385
166 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
167 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
168 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
169 libR.dylib                    	0x000000010b348541 Rf_eval + 385
170 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
171 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
172 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
173 libR.dylib                    	0x000000010b348541 Rf_eval + 385
174 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
175 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
176 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
177 libR.dylib                    	0x000000010b348541 Rf_eval + 385
178 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
179 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
180 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
181 libR.dylib                    	0x000000010b348541 Rf_eval + 385
182 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
183 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
184 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
185 libR.dylib                    	0x000000010b348541 Rf_eval + 385
186 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
187 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
188 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
189 libR.dylib                    	0x000000010b348541 Rf_eval + 385
190 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
191 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
192 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
193 libR.dylib                    	0x000000010b348541 Rf_eval + 385
194 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
195 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
196 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
197 libR.dylib                    	0x000000010b348541 Rf_eval + 385
198 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
199 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
200 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
201 libR.dylib                    	0x000000010b348541 Rf_eval + 385
202 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
203 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
204 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
205 libR.dylib                    	0x000000010b348541 Rf_eval + 385
206 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
207 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
208 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
209 libR.dylib                    	0x000000010b348541 Rf_eval + 385
210 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
211 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
212 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
213 libR.dylib                    	0x000000010b348541 Rf_eval + 385
214 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
215 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
216 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
217 libR.dylib                    	0x000000010b348541 Rf_eval + 385
218 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
219 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
220 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
221 libR.dylib                    	0x000000010b348541 Rf_eval + 385
222 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
223 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
224 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
225 libR.dylib                    	0x000000010b348541 Rf_eval + 385
226 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
227 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
228 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
229 libR.dylib                    	0x000000010b348541 Rf_eval + 385
230 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
231 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
232 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
233 libR.dylib                    	0x000000010b348541 Rf_eval + 385
234 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
235 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
236 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
237 libR.dylib                    	0x000000010b348541 Rf_eval + 385
238 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
239 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
240 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
241 libR.dylib                    	0x000000010b348541 Rf_eval + 385
242 libR.dylib                    	0x000000010b366f4c forcePromise + 172 (eval.c:557)
243 libR.dylib                    	0x000000010b3728ca getvar + 778 (eval.c:5165)
244 libR.dylib                    	0x000000010b34c90c bcEval + 15500 (eval.c:6851)
245 libR.dylib                    	0x000000010b348541 Rf_eval + 385
246 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
247 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
248 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
249 libR.dylib                    	0x000000010b348541 Rf_eval + 385
250 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
251 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
252 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
253 libR.dylib                    	0x000000010b348541 Rf_eval + 385
254 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
255 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
256 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
257 libR.dylib                    	0x000000010b348541 Rf_eval + 385
258 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
259 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
260 libR.dylib                    	0x000000010b34f728 bcEval + 27304 (eval.c:7069)
261 libR.dylib                    	0x000000010b348541 Rf_eval + 385
262 libR.dylib                    	0x000000010b368a71 R_execClosure + 2193
263 libR.dylib                    	0x000000010b367849 Rf_applyClosure + 473 (eval.c:1814)
264 libR.dylib                    	0x000000010b348a16 Rf_eval + 1622 (eval.c:846)
265 libR.dylib                    	0x000000010b39dcba Rf_ReplIteration + 810 (main.c:264)
266 libR.dylib                    	0x000000010b39f1df run_Rmainloop + 207 (main.c:1113)
267 R                             	0x000000010b286f5b main + 27
268 libdyld.dylib                 	0x00007fff691a7cc9 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x000000010b784000  rcx: 0x0000000000000000  rdx: 0x00000000000007c8
  rdi: 0x000000010b784000  rsi: 0x00007ffee4948650  rbp: 0x00007ffee4948030  rsp: 0x00007ffee4948030
   r8: 0x0000000000000007   r9: 0x0000000000000000  r10: 0x0000000000000001  r11: 0x0000000000000202
  r12: 0x0000000000000000  r13: 0x0000000000000007  r14: 0x00000000000007c8  r15: 0x00007fb48bce9d30
  rip: 0x0000000110edf430  rfl: 0x0000000000010246  cr2: 0x000000010b784000
  
Logical CPU:     2
Error Code:      0x00000004 (no mapping for user data read)
Trap Number:     14


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    0x7fff691d2000 -     0x7fff691d2ff7  liblaunch.dylib (1738.120.8) <07CF647B-F9DC-3907-AD98-2F85FCB34A72> /usr/lib/system/liblaunch.dylib
    0x7fff691d3000 -     0x7fff691d8ff7  libmacho.dylib (959.0.1)  /usr/lib/system/libmacho.dylib
    0x7fff691d9000 -     0x7fff691dbff3  libquarantine.dylib (110.40.3)  /usr/lib/system/libquarantine.dylib
    0x7fff691dc000 -     0x7fff691ddff7  libremovefile.dylib (48)  /usr/lib/system/libremovefile.dylib
    0x7fff691de000 -     0x7fff691f5ff3  libsystem_asl.dylib (377.60.2) <1170348D-2491-33F1-AA79-E2A05B4A287C> /usr/lib/system/libsystem_asl.dylib
    0x7fff691f6000 -     0x7fff691f6ff7  libsystem_blocks.dylib (74) <7AFBCAA6-81BE-36C3-8DB0-AAE0A4ACE4C5> /usr/lib/system/libsystem_blocks.dylib
    0x7fff691f7000 -     0x7fff6927efff  libsystem_c.dylib (1353.100.2) <935DDCE9-4ED0-3F79-A05A-A123DDE399CC> /usr/lib/system/libsystem_c.dylib
    0x7fff6927f000 -     0x7fff69282ffb  libsystem_configuration.dylib (1061.120.2)  /usr/lib/system/libsystem_configuration.dylib
    0x7fff69283000 -     0x7fff69286fff  libsystem_coreservices.dylib (114) <3D0A3AA8-8415-37B2-AAE3-66C03BCE8B55> /usr/lib/system/libsystem_coreservices.dylib
    0x7fff69287000 -     0x7fff6928ffff  libsystem_darwin.dylib (1353.100.2) <6EEC9975-EE3B-3C95-AA5B-030FD10587BC> /usr/lib/system/libsystem_darwin.dylib
    0x7fff69290000 -     0x7fff69297fff  libsystem_dnssd.dylib (1096.100.3) <0115092A-E61B-317D-8670-41C7C34B1A82> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff69298000 -     0x7fff69299ffb  libsystem_featureflags.dylib (17)  /usr/lib/system/libsystem_featureflags.dylib
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    0x7fff69315000 -     0x7fff6935cfff  libsystem_m.dylib (3178) <436CFF76-6A99-36F2-A3B6-8D017396A050> /usr/lib/system/libsystem_m.dylib
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    0x7fff69385000 -     0x7fff69392ffb  libsystem_networkextension.dylib (1095.120.6) <6DE86DB0-8CD2-361E-BD6A-A34282B47847> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff69393000 -     0x7fff6939cff7  libsystem_notify.dylib (241.100.2) <7E9E2FC8-DF26-340C-B196-B81B11850C46> /usr/lib/system/libsystem_notify.dylib
    0x7fff6939d000 -     0x7fff693a5fef  libsystem_platform.dylib (220.100.1) <736920EA-6AE0-3B1B-BBDA-7DCDF0C229DF> /usr/lib/system/libsystem_platform.dylib
    0x7fff693a6000 -     0x7fff693b0fff  libsystem_pthread.dylib (416.100.3) <77488669-19A3-3993-AD65-CA5377E2475A> /usr/lib/system/libsystem_pthread.dylib
    0x7fff693b1000 -     0x7fff693b5ff3  libsystem_sandbox.dylib (1217.120.7) <20C93D69-6452-3C82-9521-8AE54345C66F> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff693b6000 -     0x7fff693b8fff  libsystem_secinit.dylib (62.100.2)  /usr/lib/system/libsystem_secinit.dylib
    0x7fff693b9000 -     0x7fff693c0ffb  libsystem_symptoms.dylib (1238.120.1) <25C3866B-004E-3621-9CD3-B1E9C4D887EB> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff693c1000 -     0x7fff693d7ff2  libsystem_trace.dylib (1147.120)  /usr/lib/system/libsystem_trace.dylib
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External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 8
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 192821905
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=656.7M resident=0K(0%) swapped_out_or_unallocated=656.7M(100%)
Writable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Activity Tracing                   256K        1 
Kernel Alloc Once                    8K        1 
MALLOC                           383.1M       67 
MALLOC guard page                   24K        4 
MALLOC_MEDIUM (reserved)         664.0M        6         reserved VM address space (unallocated)
STACK GUARD                       56.0M        1 
Stack                             8192K        1 
VM_ALLOCATE                          4K        1 
__DATA                            26.9M      375 
__DATA_CONST                        20K        1 
__FONT_DATA                          4K        1 
__LINKEDIT                       402.4M       98 
__OBJC_RO                         32.2M        1 
__OBJC_RW                         1892K        2 
__TEXT                           254.3M      343 
__UNICODE                          564K        1 
mapped file                       27.2M        4 
shared memory                       12K        3 
===========                     =======  ======= 
TOTAL                              1.8G      911 
TOTAL, minus reserved VM space     1.2G      911 

[slowkow]

Paul, I tried your binary and it also failed with a similar error.

> devtools::install_local("~/Downloads/Seurat_3.2.0.tgz")
Skipping 1 packages ahead of CRAN: data.table
* installing *binary* package ‘Seurat’ ...
* DONE (Seurat)
> library(Seurat)
Killed: 9

This also gave Namespace CODESIGNING, Code 0x2 in the Console Crash Report logs.

[KatherineMueller]

Hello,

I am having similar issues installing. I'm running R version 4.0.2 on MacOS Catalina 10.15.5. Here's what happens when I initially try the install:

Installing package into ‘/Users/katherinemueller/Library/R/4.0/library’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
       binary source needs_compilation
Seurat  3.1.5  3.2.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘Seurat’

trying URL 'https://cran.rstudio.com/src/contrib/Seurat_3.2.0.tar.gz'
Content type 'application/x-gzip' length 1482089 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

ERROR: failed to lock directory ‘/Users/katherinemueller/Library/R/4.0/library’ for modifying
Try removing ‘/Users/katherinemueller/Library/R/4.0/library/00LOCK-Seurat’
Warning in install.packages :
  installation of package ‘Seurat’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/xt/k6t8jllx42z65jp6_f136ps00000gn/T/RtmpiTTpHt/downloaded_packages’
> 

When I delete this mystery "00LOCK-Seurat" folder and try again, I get the following:

Installing package into ‘/Users/katherinemueller/Library/R/4.0/library’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
       binary source needs_compilation
Seurat  3.1.5  3.2.0              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘Seurat’

trying URL 'https://cran.rstudio.com/src/contrib/Seurat_3.2.0.tar.gz'
Content type 'application/x-gzip' length 1482089 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘Seurat’ ...
** package ‘Seurat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c ModularityOptimizer.cpp -o ModularityOptimizer.o
ModularityOptimizer.cpp:762:7: warning: unused variable 'n2_max' [-Wunused-variable]
  int n2_max = *std::max_element(node2.cbegin(), node2.cend());
      ^
ModularityOptimizer.cpp:761:7: warning: unused variable 'n1_max' [-Wunused-variable]
  int n1_max = *std::max_element(node1.cbegin(), node1.cend());
      ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RModularityOptimizer.cpp -o RModularityOptimizer.o
In file included from RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 RModularityOptimizer.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c data_manipulation.cpp -o data_manipulation.o
In file included from data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 data_manipulation.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c integration.cpp -o integration.o
In file included from integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 integration.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c snn.cpp -o snn.o
In file included from snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:535:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Geometry:58:

> /Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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 snn.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.0/Resources/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++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Seurat.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o data_manipulation.o integration.o snn.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/katherinemueller/Library/R/4.0/library/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 63386 Done                    echo 'tools:::.install_packages()'
     63387 Killed: 9               | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --no-echo --args ${args}
Warning in install.packages :
  installation of package ‘Seurat’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/xt/k6t8jllx42z65jp6_f136ps00000gn/T/RtmpiTTpHt/downloaded_packages’

I get the same results when I try to install directly from the terminal. The weirdest thing is that I haven't updated my version of R in the last few days, and Seurat was running just fine yesterday - I believe I may have accidentally tried to update Seurat yesterday while installing another program ('fgsea'), which is when it broke for me.

Thank you in advance for your help with this! Seurat is a great package, and I appreciate any feedback you can offer to help me get it up and running again.

[Projectnix]

I had the same issue and I was able to resolve this issue through following this https://github.com/rmacoslib/r-macos-rtools/releases/tag/v4.0.0

I was unable to compile RcppArmadillo, deldir, and Seurat. After following the linked github page for macos-rtools, I still got 17 warnings when trying to compile Seurat 3.2.0, but it compiled fine and I was able to load the library and continue my work. As far as I understand this issue happens due to misaligned headers between R, R-tools for mac, and Xcode. Hope this helps!

[KatherineMueller]

Thanks for the suggestion @Projectnix ! No luck unfortunately - I just tried installing r-macos-rtools, and while it seems to have installed successfully I'm still seeing the same errors during Seurat install as before, even after restarting the R session.

[slowkow]

@Projectnix I followed the same steps without success (install Xcode, install gfortran, remove ~/.R/Makevars). It's neat that someone packaged those steps into a GUI, but we can also run each of them manually from the command line. After completing all of the steps, I still get Killed: 9 when trying to load the binary Seurat or when trying to compile the source Seurat.

---

I found a fix on my system!!

I hope that it works for others, too.

This is it:

mv ~/miniconda3 ~/miniconda3.bak
R -e 'install.packages(c("deldir", "Seurat"))'

The installation completes and I can run library(Seurat) successfully without getting Killed: 9.

It seems that R and Anaconda (or miniconda) do not get along if Intel MKL is invited to the party. If we kick MKL out, then R and Anaconda can live happily ever after.

So, if you want to keep miniconda, then this should work (but you need to execute this in every conda environment 😭):

conda uninstall mkl

Major bummer: uninstalling mkl gets rid of numpy, scipy, matplotlib, biopython, deeptools, and pybigwig.

If anyone has ideas on how to get MKL to stop crashing R, that would be great! 🤞

---

Why did this happen?

I checked the crash logs again (in my previous post above) and noticed this:

Application Specific Information:
dyld: in dlopen()
/Users/kamil/miniconda3/lib/libmkl_intel_thread.dylib

This issue from the RStudio reticulate package has exactly the same error in the crash log.

@kevinushey says:

the application is crashing because the code signature in the version of Intel MKL being loaded is invalid.

(I don't understand what Kevin said.) Maybe R is checking the signature of the Intel MKL library and it doesn't match what R expects to see?

For posterity, here is the code signature for my Intel MKL file. I don't know how to fix it.

$ codesign -dv --verbose=4 /Users/kamil/miniconda3/lib/libmkl_intel_thread.dylib
Executable=/Users/kamil/miniconda3/lib/libmkl_intel_thread.dylib
Identifier=libmkl_intel_thread.dylib
Format=Mach-O thin (x86_64)
CodeDirectory v=20200 size=369017 flags=0x10000(runtime) hashes=11527+2 location=embedded
VersionPlatform=1
VersionMin=658432
VersionSDK=658432
Hash type=sha256 size=32
CandidateCDHash sha256=9fae015418c823a6a5bdd36af6cb8875bdb6b98f
CandidateCDHashFull sha256=9fae015418c823a6a5bdd36af6cb8875bdb6b98fbf4d3146fa647b2cf5b51acb
Hash choices=sha256
CMSDigest=9fae015418c823a6a5bdd36af6cb8875bdb6b98fbf4d3146fa647b2cf5b51acb
CMSDigestType=2
Page size=4096
CDHash=9fae015418c823a6a5bdd36af6cb8875bdb6b98f
Signature size=8643
Authority=Developer ID Application: Intel Corporation Apps (Z3L495V9L4)
Authority=Developer ID Certification Authority
Authority=Apple Root CA
Timestamp=Aug 8, 2019 at 8:01:09 AM
Info.plist=not bound
TeamIdentifier=Z3L495V9L4
Sealed Resources=none
Internal requirements count=2 size=176

[Projectnix]

@slowkow @KatherineMueller I forgot to mention that after I ran that mac-rtools update and before I installed Seurat, I first did install.packages(c("deldir", "RcppArmadillo")). I allowed those to be compiled rather than a binary install and it worked, unlike before the mac-rtools fix. After those 2 installed by being compiled, I installed Seurat 3.2.0 from the source and it compiled fine. I think there's something tied to deldir in particular that prevents Seurat from being compiled properly unless deldir is the latest version (0.1-28).

[rhondabacher]

Aha! This finally worked for me! (the mac-rtools then deldir and RcppArmadillo and Seurat--all with 'no' to the "Do you want to install from sources the package which needs compilation?"

Thanks @Projectnix !

[KatherineMueller]

@Projectnix wow, that solved it, just as @rhondabacher describes! I'm confused by the fix since to my knowledge I had neither deldir nor RcppArmadillo installed prior, but I seem to be running without issue now. Thank you so much for sending in that fix!

[slowkow]

For anyone who is having issues with miniconda like me, this might help (thanks to Cami Williams):

conda install nomkl numpy scipy scikit-learn numexpr
conda remove mkl mkl-service

Now I can install and load Seurat without Killed: 9 caused by the weird MKL thing.

This is much better than disabling miniconda with mv ~/.miniconda{,.bak}. We can keep our packages, but just kick MKL out.

[carloelle]

I followed your suggestions (installed mac-rtools, RcppArmadillo, deldir) and I managed to install Seurat in RStudio.
Anyway I fail to load it:

library(Seurat) Error: package or namespace load failed for ‘Seurat’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so': dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so, 6): Symbol not found: _EXTPTR_PTR Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so Expected in: /Library/Frameworks/R.framework/Resources/lib/libR.dylib in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so Warning message: package ‘Seurat’ was built under R version 4.0.2

It gives the same error (Symbol not found: _EXTPTR_PTR) also when I try to load other libraries (such as RcppArmadillo). Anyone has ever had the same issue? How did you overcome it? Thanks!

sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

---

Nevermind, the error disappears as soon as I delete and reinstall R and RStudio

[mojaveazure]

Hi all,

Sorry for the delay. Glad you managed to find a solution to not being able to install Seurat, and many thanks to @slowkow for diagnosing the issue!

For anyone else who has difficulty install Seurat on a system with conda installed, please see #3273 (comment)

[slowkow]

@kmuench Could I please ask if you were able to install Seurat? I wonder if your Crash Logs look the same as mine (mkl in the log) or if they're different... maybe I'm the only one with the MKL issue?

@mojaveazure I think there might be multiple different issues here that could result in similar error messages:

• For me, MKL seems to be the cause for the installation issue.
• For @Projectnix, @KatherineMueller, @rhondabacher, they might have had some other issue, and I don't know why installing deldir and RcppArmadillo fixes it.

I also don't understand why installations on Travis and GitHub Actions succeeded, but our own installations failed. 🤷‍♂️

[mojaveazure]

@slowkow We do not use conda on any CI system or any of our own machines, instead opting to install R and other system dependencies from official sources (eg. CRAN, APT, etc). We've found conda to cause too many issues with R, Seurat, and reticulate (used previously for running UMAP, currently for leiden clustering). These issues range from not working with CRAN versions of Rcpp or Rcpp-related packages, removing and hiding the compiler from R, and prevent R/reticulate from finding Python modules. As such, we generally recommend not using conda, instead using alternatives such as:

• virtual environments in Python/renv in R for environments,
• pip/install.packages for obtaining Python/R packages
• brew/a package manager for installing system packages and libraries

For the MKL issue: any and all MKL issues we've seen Seurat have been associated with conda. We have successfully run Seurat using MRO, which includes MKL

For the RcppArmadillo issues, I expect that hese users have conda on their system and removing it will fix their issues. If they do not have conda on their system, or removing it doesn't solve their issue, I will reopen and we can continue debugging

[kmuench]

@slowkow Just returned to this - I don't have conda installed, and the (1)install.packages(c("deldir", "RcppArmadillo") (2) https://github.com/rmacoslib/r-macos-rtools/releases/tag/v4.0.0 (2) install.packages(Seurat) fix worked for me with no errors at all on second run. Thanks for your in-depth troubleshoot though!

[KatherineMueller]

@slowkow my case was the same as @kmuench, I'm not running through conda and the same above fix worked for me. I'm perplexed because I had neither package installed to begin with prior to the issues, but I have not had problems running Seurat since.

[slowkow]

@kmuench @KatherineMueller Interesting! Thanks for sharing.

@mojaveazure It seems that conda might not be the cause of this issue for many users... I can't explain it.