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All 3 knit options fail after v4 upgrade on mac #2170

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splaisan opened this issue Jun 19, 2021 · 5 comments
Closed

All 3 knit options fail after v4 upgrade on mac #2170

splaisan opened this issue Jun 19, 2021 · 5 comments
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bug an unexpected problem or unintended behavior duplicate already another issue about this

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@splaisan
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MacOS 10.14.6
RStudio 1.4.1717 (fresh reinstall)
R 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Latex 2021 (fresh reinstall also tried)

  • I tried install and reinstall tinytex without more success (and restarted RStudio several times after installs.

Reproducible error after loading the demo RMD for any kind of knitting (tried all three, same error)

When I knit the built-in demo Rmd code I get:

sh: rmarkdown::render: command not found
Warning message:
In system(paste0("rmarkdown::render \"", input, "\"")) :
  error in running command

Can you please suggest other things to fix this, it used to work perfectly before R4 and the latest RStudio (both upgraded together).

Thanks in advance

PS: the same R and RStudio versions work like a charm on my ubuntu server
@cderv
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cderv commented Jun 19, 2021

Hi @splaisan,

I think this is related to this is a duplicate of #1990

This error is thrown by RStudio IDE and we already opened an issue there (rstudio/rstudio#9435)

it can happen when rmarkdown is not correctly installed and can't be loaded.

library("rmarkdown")

should not work as expected too probably.

You may try reinstall the rmarkdown packages, tries to load it in R (library("rmarkdown")) and check it works correctly (for example use rmarkdown::render() in R console to render a document).

After that, the RStudio IDE should correctly use it.

Sorry for the inconvenience.

@cderv cderv added duplicate already another issue about this bug an unexpected problem or unintended behavior labels Jun 19, 2021
@splaisan
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splaisan commented Jun 19, 2021 •
edited
Loading

Thanks for the answer.
I de-installed markdown and rmarkdown and started to reinstall them.
The installer tried to update other dependencies ('dplyr', 'plotly', 'Seurat', 'sparklyr', 'spatstat.core') and failed for dplyr

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/opt/R_LIBS/rlang/libs/rlang.so':
  dlopen(/opt/R_LIBS/rlang/libs/rlang.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
  Referenced from: /opt/R_LIBS/rlang/libs/rlang.so
  Reason: image not found
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘dplyr’

It seems that R4 is missing libraries or source files required for these packages (and maybe also for rmarkdown)
Could it be that Rv4 itself has a problem?

After reinstalling markdown and rmarkdown (1.1 and 2.9) I still get the error when I knit.

This also fails, again blaming libR.dylib

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


rmarkdown::render()
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/opt/R_LIBS/digest/libs/digest.so':
  dlopen(/opt/R_LIBS/digest/libs/digest.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
  Referenced from: /opt/R_LIBS/digest/libs/digest.so
  Reason: image not found

Best

====== reinstall output =========

I attach the long output below.

> remove.packages("rmarkdown")
Removing package from ‘/opt/R_LIBS’
(as ‘lib’ is unspecified)
> install("rmarkdown")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'rmarkdown'
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rmarkdown_2.9.tgz'
Content type 'application/x-gzip' length 3635709 bytes (3.5 MB)
==================================================
downloaded 3.5 MB


The downloaded binary packages are in
	/opt/R_LIBS/tmp/Rtmp66DmiQ/downloaded_packages
Old packages: 'dplyr', 'plotly', 'Seurat', 'sparklyr', 'spatstat.core'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
       binary  source needs_compilation
dplyr   1.0.6   1.0.7              TRUE
plotly  4.9.4 4.9.4.1             FALSE
Seurat  4.0.1   4.0.3              TRUE

Do you want to install from sources the packages which need compilation? (Yes/no/cancel) 
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sparklyr_1.7.1.tgz'
Content type 'application/x-gzip' length 5735495 bytes (5.5 MB)
==================================================
downloaded 5.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/spatstat.core_2.2-0.tgz'
Content type 'application/x-gzip' length 6753765 bytes (6.4 MB)
==================================================
downloaded 6.4 MB


The downloaded binary packages are in
	/opt/R_LIBS/tmp/Rtmp66DmiQ/downloaded_packages
installing the source packages ‘dplyr’, ‘plotly’, ‘Seurat’

trying URL 'https://cran.rstudio.com/src/contrib/dplyr_1.0.7.tar.gz'
Content type 'application/x-gzip' length 852103 bytes (832 KB)
==================================================
downloaded 832 KB

trying URL 'https://cran.rstudio.com/src/contrib/plotly_4.9.4.1.tar.gz'
Content type 'application/x-gzip' length 3742653 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://cran.rstudio.com/src/contrib/Seurat_4.0.3.tar.gz'
Content type 'application/x-gzip' length 1457139 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c chop.cpp -o chop.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c filter.cpp -o filter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c funs.cpp -o funs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c group_by.cpp -o group_by.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c group_data.cpp -o group_data.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c imports.cpp -o imports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mask.cpp -o mask.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mutate.cpp -o mutate.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c slice.cpp -o slice.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c summarise.cpp -o summarise.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /opt/R_LIBS/00LOCK-dplyr/00new/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/opt/R_LIBS/rlang/libs/rlang.so':
  dlopen(/opt/R_LIBS/rlang/libs/rlang.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
  Referenced from: /opt/R_LIBS/rlang/libs/rlang.so
  Reason: image not found
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘dplyr’
* removing ‘/opt/R_LIBS/dplyr’
* restoring previous ‘/opt/R_LIBS/dplyr’
* installing *source* package ‘plotly’ ...
** package ‘plotly’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘ggplot2’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/opt/R_LIBS/rlang/libs/rlang.so':
  dlopen(/opt/R_LIBS/rlang/libs/rlang.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
  Referenced from: /opt/R_LIBS/rlang/libs/rlang.so
  Reason: image not found
Error: package ‘ggplot2’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘plotly’
* removing ‘/opt/R_LIBS/plotly’
* restoring previous ‘/opt/R_LIBS/plotly’
* 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'/opt/R_LIBS/Rcpp/include' -I'/opt/R_LIBS/RcppEigen/include' -I'/opt/R_LIBS/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'/opt/R_LIBS/Rcpp/include' -I'/opt/R_LIBS/RcppEigen/include' -I'/opt/R_LIBS/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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:1:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Core:540:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:2:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/LU:47:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:12:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Jacobi:29:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:15:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Householder:27:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:5:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SVD:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:6:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Geometry:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:7:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Eigenvalues:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:26:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCore:66:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:27:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/OrderingMethods:71:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:29:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseQR:34:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:33:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/CholmodSupport:45:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:35:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:39:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:40:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:26:
In file included from /opt/R_LIBS/Rcpp/include/Rcpp.h:57:
/opt/R_LIBS/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
19 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/R_LIBS/Rcpp/include' -I'/opt/R_LIBS/RcppEigen/include' -I'/opt/R_LIBS/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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:1:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Core:540:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:2:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/LU:47:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:12:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Jacobi:29:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:15:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Householder:27:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:5:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SVD:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:6:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Geometry:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:7:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Eigenvalues:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:26:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCore:66:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:27:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/OrderingMethods:71:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:29:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseQR:34:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:33:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/CholmodSupport:45:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:35:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:39:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:40:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:26:
In file included from /opt/R_LIBS/Rcpp/include/Rcpp.h:57:
/opt/R_LIBS/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
19 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/R_LIBS/Rcpp/include' -I'/opt/R_LIBS/RcppEigen/include' -I'/opt/R_LIBS/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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:1:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Core:540:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:2:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/LU:47:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:12:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Jacobi:29:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:15:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Householder:27:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:5:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SVD:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:6:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Geometry:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:7:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Eigenvalues:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:26:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCore:66:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:27:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/OrderingMethods:71:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:29:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseQR:34:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:33:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/CholmodSupport:45:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:35:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:39:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:40:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:26:
In file included from /opt/R_LIBS/Rcpp/include/Rcpp.h:57:
/opt/R_LIBS/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
19 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/R_LIBS/Rcpp/include' -I'/opt/R_LIBS/RcppEigen/include' -I'/opt/R_LIBS/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c fast_NN_dist.cpp -o fast_NN_dist.o
In file included from fast_NN_dist.cpp:1:
In file included from /opt/R_LIBS/Rcpp/include/Rcpp.h:57:
/opt/R_LIBS/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/R_LIBS/Rcpp/include' -I'/opt/R_LIBS/RcppEigen/include' -I'/opt/R_LIBS/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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:1:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Core:540:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:2:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/LU:47:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:12:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Jacobi:29:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:15:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Householder:27:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:5:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SVD:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:6:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Geometry:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:7:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Eigenvalues:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:26:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCore:66:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:27:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/OrderingMethods:71:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:29:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseQR:34:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:33:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/CholmodSupport:45:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:35:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:39:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:40:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:26:
In file included from /opt/R_LIBS/Rcpp/include/Rcpp.h:57:
/opt/R_LIBS/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
19 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/R_LIBS/Rcpp/include' -I'/opt/R_LIBS/RcppEigen/include' -I'/opt/R_LIBS/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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:1:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Core:540:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:2:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/LU:47:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:12:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Jacobi:29:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:3:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Cholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:15:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Householder:27:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:4:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/QR:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:5:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SVD:48:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:6:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Geometry:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:30:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Dense:7:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Eigenvalues:58:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:26:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCore:66:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:27:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/OrderingMethods:71:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:29:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseCholesky:43:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/SparseQR:34:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:31:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/Sparse:33:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:32:
In file included from /opt/R_LIBS/RcppEigen/include/Eigen/CholmodSupport:45:
/opt/R_LIBS/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:35:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:39:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:25:
In file included from /opt/R_LIBS/RcppEigen/include/RcppEigenForward.h:40:
In file included from /opt/R_LIBS/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/opt/R_LIBS/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: 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 /opt/R_LIBS/RcppEigen/include/RcppEigen.h:26:
In file included from /opt/R_LIBS/Rcpp/include/Rcpp.h:57:
/opt/R_LIBS/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
19 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/opt/R_LIBS/Rcpp/include' -I'/opt/R_LIBS/RcppEigen/include' -I'/opt/R_LIBS/RcppProgress/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c valid_pointer.c -o valid_pointer.o
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 fast_NN_dist.o integration.o snn.o valid_pointer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /opt/R_LIBS/00LOCK-Seurat/00new/Seurat/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/opt/R_LIBS/RANN/libs/RANN.so':
  dlopen(/opt/R_LIBS/RANN/libs/RANN.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
  Referenced from: /opt/R_LIBS/RANN/libs/RANN.so
  Reason: image not found
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘Seurat’
* removing ‘/opt/R_LIBS/Seurat’
* restoring previous ‘/opt/R_LIBS/Seurat’

The downloaded source packages are in
	‘/opt/R_LIBS/tmp/Rtmp66DmiQ/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘dplyr’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘plotly’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘Seurat’ had non-zero exit status

@splaisan
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I found that I messed up my R library when I upgraded R to v4. I probably kept R v3 libraries conflicting with R v4

I did a clean install of R and it now works, I can knit again.

I will now reinstall all my R v3 libraries in their current version using biocmanager.

Hope for the best
Sorry for the report, it was my fault after all (as often :-)

@cderv
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cderv commented Jun 19, 2021

No worries!

From what I know, When you upgrade R to a new major version (3.6.3 to 4.0 for example) you need to reinstall all packages. At least this is greatly advised! R default user lib even have the major + minor version in there path usually.

And this is not an issue with Rmarkdown only. It could mean some problem with other package.

Glad it works now!

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