Openssl install failure on MacOS Monterey M1 (arm64) for R 4.2.0 ("Vigorous Calisthenics") #101

cmhatche23 · 2022-05-16T19:20:04Z

Hi,

I recently upgraded my R version to the latest release (4.2.0, 2022-04-22). I am receiving this error message when installing openssl package. I have tried installing from both CRAN and GitHub:

R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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> devtools::install_github("jeroen/openssl")
Downloading GitHub repo jeroen/openssl@HEAD
✔  checking for file ‘/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpjQXYpT/remotes1311770b98515/jeroen-openssl-47bf18b/DESCRIPTION’ ...
─  preparing ‘openssl’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘openssl_2.0.1.tar.gz’
   
* installing *source* package ‘openssl’ ...
** using staged installation
Using PKG_CFLAGS=-I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include
Using PKG_LIBS=-L/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/lib -lssl -lcrypto
** libs
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c aes.c -o aes.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c base64.c -o base64.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c bignum.c -o bignum.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cert.c -o cert.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c compatibility.c -o compatibility.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c diffie.c -o diffie.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c envelope.c -o envelope.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c error.c -o error.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c hash.c -o hash.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c info.c -o info.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c keygen.c -o keygen.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c keys.c -o keys.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c onload.c -o onload.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c openssh.c -o openssh.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c password.c -o password.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pbkdf.c -o pbkdf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pem.c -o pem.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pkcs12.c -o pkcs12.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pkcs7.c -o pkcs7.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rand.c -o rand.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rsa.c -o rsa.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c signing.c -o signing.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c ssl.c -o ssl.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c stream.c -o stream.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c write.c -o write.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c x25519.c -o x25519.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c bcrypt/blowfish.c -o bcrypt/blowfish.o
ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/[email protected]/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -L/private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/lib -lssl -lcrypto -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/opt/[email protected]/lib'
ld: warning: ignoring file /private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/lib/libcrypto.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
ld: warning: ignoring file /private/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T/RtmpOrSTix/R.INSTALL131a33d271a4b/openssl/.deps/lib/libssl.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
installing to /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-openssl/00new/openssl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘openssl’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-openssl/00new/openssl/libs/openssl.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/00LOCK-openssl/00new/openssl/libs/openssl.so, 0x0006): symbol not found in flat namespace '_ASN1_STRING_to_UTF8'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/openssl’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/5d/z3_6_g1d6d91v4ppjkh4ldnh0000gn/T//RtmpjQXYpT/file13117452ee57a/openssl_2.0.1.tar.gz’ had non-zero exit status

Current session Info:

> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13   magrittr_2.0.3    usethis_2.1.5     devtools_2.4.3    pkgload_1.2.4     R6_2.5.1         
 [7] rlang_1.0.2       fastmap_1.1.0     tools_4.2.0       pkgbuild_1.3.1    sessioninfo_1.2.2 cli_3.3.0        
[13] withr_2.5.0       ellipsis_0.3.2    remotes_2.4.2     rprojroot_2.0.3   lifecycle_1.0.1   crayon_1.5.1     
[19] brio_1.1.3        processx_3.5.3    purrr_0.3.4       callr_3.7.0       fs_1.5.2          ps_1.7.0         
[25] curl_4.3.2        testthat_3.1.4    memoise_2.0.1     glue_1.6.2        cachem_1.0.6      compiler_4.2.0   
[31] desc_1.4.1        prettyunits_1.1.1

I have [email protected] installed on my machine with homebrew, with the following configurations in my ~/.zshrc file:

### openssl:
path+=("/opt/homebrew/opt/[email protected]/bin")
#path+=("/opt/homebrew/opt/openssl@3/bin")
export LDFLAGS="-L/opt/homebrew/opt/[email protected]/lib"
export CPPFLAGS="-I/opt/homebrew/opt/[email protected]/include"
#export LDFLAGS="-L/opt/homebrew/opt/openssl@3/lib"
export PKG_CONFIG_PATH="/opt/homebrew/opt/[email protected]/lib/pkgconfig"
export LD_LIBRARY_PATH="/opt/homebrew/opt/[email protected]/lib"
# export PKG_CONFIG_PATH="/opt/homebrew/opt/openssl@3/lib/pkgconfig"
export RUBY_CONFIGURE_OPTS="--with-openssl-dir=/opt/homebrew/opt/[email protected]"

Any ideas? I noticed the issue about a week after downloading and installing the new R version when I tried using the googlesheets4 package.

The text was updated successfully, but these errors were encountered:

jeroen · 2022-05-16T20:02:42Z

That is certainly wierd. What do you get for these in your shell:

arch

which pkg-config

pkg-config --modversion libssl

cmhatche23 · 2022-05-16T21:16:05Z

@jeroen

Here is what I get from each of those commands:

❯ arch                                                                               ─╯
arm64

❯ which pkg-config                                                                   ─╯
/opt/homebrew/bin/pkg-config

pkg-config --modversion libssl                                                     ─╯
1.1.1o

Thanks in advance.

michalovadek · 2022-05-25T09:48:17Z

hi, not sure whether this is related but perhaps might be.

R-CMD-CHECK for my package is failing due to openssl not building from source on windows-latest. Log from Github Actions:

Error: Error: <callr_remote_error: Failed to build source package 'openssl'>
   in process 6552 
  -->
  Failed to build source package 'openssl', stdout + stderr:
  
  OE> * installing *source* package 'openssl' ...
  OE> ** package 'openssl' successfully unpacked and MD5 sums checked
  OE> staged installation is only possible with locking
  OE> ** using non-staged installation
  OE> ** libs
  OE> "C:/R/bin/x64/Rscript.exe" "../tools/winlibs.R" 1.1.1k
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c aes.c -o aes.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c base64.c -o base64.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c bignum.c -o bignum.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c cert.c -o cert.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c compatibility.c -o compatibility.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c diffie.c -o diffie.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c envelope.c -o envelope.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c error.c -o error.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c hash.c -o hash.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c info.c -o info.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c keygen.c -o keygen.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c keys.c -o keys.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c onload.c -o onload.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c openssh.c -o openssh.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c password.c -o password.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c pbkdf.c -o pbkdf.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c pem.c -o pem.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c pkcs12.c -o pkcs12.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c pkcs7.c -o pkcs7.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c rand.c -o rand.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c rsa.c -o rsa.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c signing.c -o signing.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c ssl.c -o ssl.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c stream.c -o stream.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c write.c -o write.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c x25519.c -o x25519.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
  OE> gcc  -I"C:/R/include" -DNDEBUG -I../windows/openssl-1.1.1k/include    -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -Wall -pedantic -c bcrypt/blowfish.c -o bcrypt/blowfish.o
  OE> ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
  OE> gcc -shared -s -static-libgcc -o openssl.dll tmp.def aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -L../windows/openssl-1.1.1k/lib/x64-ucrt -lssl -lcrypto -lws2_32 -lgdi32 -lcrypt32 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LC:/R/bin/x64 -lR
  OE> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../windows/openssl-1.1.1k/lib/x64-ucrt/libcrypto.a(v3_utl.o):(.text+0xd2a): undefined reference to `__stdio_common_vsscanf'
  OE> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../windows/openssl-1.1.1k/lib/x64-ucrt/libcrypto.a(e_capi.o):(.text+0x3700): undefined reference to `__imp___acrt_iob_func'
  OE> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../windows/openssl-1.1.1k/lib/x64-ucrt/libcrypto.a(eng_openssl.o):(.text+0x12): undefined reference to `__imp___acrt_iob_func'
  OE> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../windows/openssl-1.1.1k/lib/x64-ucrt/libcrypto.a(eng_openssl.o):(.text+0x266): undefined reference to `__imp___acrt_iob_func'
  OE> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../windows/openssl-1.1.1k/lib/x64-ucrt/libcrypto.a(ui_openssl.o):(.text+0x19): undefined reference to `__imp___acrt_iob_func'
  OE> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../windows/openssl-1.1.1k/lib/x64-ucrt/libcrypto.a(ui_openssl.o):(.text+0x174): undefined reference to `__imp___acrt_iob_func'
  OE> C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: ../windows/openssl-1.1.1k/lib/x64-ucrt/libcrypto.a(ui_openssl.o):(.text+0x197): more undefined references to `__imp___acrt_iob_func' follow
  OE> collect2.exe: error: ld returned 1 exit status
  OE> no DLL was created
  OE> ERROR: compilation failed for package 'openssl'
  OE> * removing 'C:/Users/RUNNER~1/AppData/Local/Temp/Rtmp2FMxQh/pkg-lib19982ffe7cb3/openssl'
  
   Stack trace:
  
   12. (function (...)  ...
   13. base:::withCallingHandlers(cli_message = function(msg) { ...
   14. get("pkg_install_do_plan", asNamespace("pak"))(...)
   15. pkgdepends::install_package_plan(plan = plan, lib = lib, num_workers = num_ ...
   16. base:::withCallingHandlers({ ...
   17. pkgdepends:::handle_events(state, events)
   18. pkgdepends:::handle_event(state, i)
   19. pkgdepends:::stop_task(state, worker)
   20. pkgdepends:::stop_task_build(state, worker)
   21. base:::throw(new_pkg_build_error("Failed to build source package {pkg}",  ...
   22. base:::signalCondition(cond)
   23. (function (e)  ...
   24. base:::stop(e)
   25. (function (e)  ...
  
   x Failed to build source package 'openssl'

can-taslicukur · 2022-12-07T08:21:13Z

I have the same problem for MacOS Ventura M1 (arm64) R 4.2.2
I installed [email protected] via homebrew and have tried exporting PKG_CONFIG_PATH. This is what I get when I try to install openssl with renv.

> install.packages("openssl")
Retrieving 'https://packagemanager.rstudio.com/all/latest/src/contrib/openssl_2.0.4.tar.gz' ...
	OK [file is up to date]
Installing openssl [2.0.4] ...
	FAILED
Error installing package 'openssl':
===================================
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
** using staged installation
Homebrew 3.6.14
Homebrew/homebrew-core (git revision d7bde1056b7; last commit 2022-12-07)
Homebrew/homebrew-cask (git revision 6fb50d235a; last commit 2022-12-07)
Using PKG_CFLAGS=-I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include
Using PKG_LIBS=-L/usr/local/opt/openssl/lib -L/usr/local/opt/[email protected]/lib -lssl -lcrypto
** libs
rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c aes.c -o aes.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c base64.c -o base64.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c bignum.c -o bignum.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cert.c -o cert.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c compatibility.c -o compatibility.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c diffie.c -o diffie.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c envelope.c -o envelope.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c error.c -o error.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c hash.c -o hash.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c info.c -o info.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c keygen.c -o keygen.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c keys.c -o keys.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c onload.c -o onload.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c openssh.c -o openssh.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c password.c -o password.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pbkdf.c -o pbkdf.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pem.c -o pem.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pkcs12.c -o pkcs12.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pkcs7.c -o pkcs7.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rand.c -o rand.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rsa.c -o rsa.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c signing.c -o signing.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c ssl.c -o ssl.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c stream.c -o stream.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c write.c -o write.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c x25519.c -o x25519.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/openssl/include -I/usr/local/opt/[email protected]/include  -I/usr/local/opt/[email protected]/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c bcrypt/blowfish.c -o bcrypt/blowfish.o
ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o
gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/[email protected]/lib -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -L/usr/local/opt/openssl/lib -L/usr/local/opt/[email protected]/lib -lssl -lcrypto -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/opt/openssl/lib'
ld: warning: -undefined dynamic_lookup may not work with chained fixups
ld: warning: ignoring file /usr/local/opt/[email protected]/lib/libssl.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
ld: warning: ignoring file /usr/local/opt/[email protected]/lib/libcrypto.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
installing to /Users/ege/Documents/rhino-showcase/renv/staging/1/00LOCK-openssl/00new/openssl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘openssl’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Users/ege/Documents/rhino-showcase/renv/staging/1/00LOCK-openssl/00new/openssl/libs/openssl.so':
  dlopen(/Users/ege/Documents/rhino-showcase/renv/staging/1/00LOCK-openssl/00new/openssl/libs/openssl.so, 0x0006): symbol not found in flat namespace '_ASN1_STRING_to_UTF8'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/ege/Documents/rhino-showcase/renv/staging/1/openssl’
Error: install of package 'openssl' failed [error code 1]
Traceback (most recent calls last):
12: install.packages("openssl")
11: install(pkgs)
10: renv_install_impl(records)
 9: renv_install_staged(records)
 8: renv_install_default(records)
 7: handler(package, renv_install_package(record))
 6: renv_install_package(record)
 5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
        vwritef("\tFAILED")
        writef(e$output)
    })
 4: renv_install_package_impl(record)
 3: r_cmd_install(package, path)
 2: r_exec_error(package, output, "install", status)
 1: stop(error)

can-taslicukur · 2022-12-29T10:19:25Z

To follow up on my previous comment, the problem was that my homebrew was installed /usr/local instead of /opt/homebrew/bin so reinstalling homebrew and installing openssl from the new installed version solved the issue

henriquesposito mentioned this issue May 26, 2022

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Openssl install failure on MacOS Monterey M1 (arm64) for R 4.2.0 ("Vigorous Calisthenics") #101

Openssl install failure on MacOS Monterey M1 (arm64) for R 4.2.0 ("Vigorous Calisthenics") #101

cmhatche23 commented May 16, 2022

jeroen commented May 16, 2022 •

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can-taslicukur commented Dec 29, 2022

Openssl install failure on MacOS Monterey M1 (arm64) for R 4.2.0 ("Vigorous Calisthenics") #101

Openssl install failure on MacOS Monterey M1 (arm64) for R 4.2.0 ("Vigorous Calisthenics") #101

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cmhatche23 commented May 16, 2022

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