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adeverse / ade4

Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
http://adeverse.github.io/ade4/
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Warning in install.packages : installation of package ‘ade4’ had non-zero exit status #32

Closed melodyoungg closed 1 year ago

melodyoungg commented 1 year ago

In trying to download this package the following error occurs. There is no stack overflow for this issue. I tried to download from online repository and downloaded the package to local disk and tried to install it locally, both failed with this issue. Please help resolve!

install.packages("ade4")

There is a binary version available but the source version is later: binary source needs_compilation ade4 1.7-20 1.7-22 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes installing the source package ‘ade4’

trying URL 'https://cran.rstudio.com/src/contrib/ade4_1.7-22.tar.gz' Content type 'application/x-gzip' length 3365194 bytes (3.2 MB)

downloaded 3.2 MB

thioulouse commented 1 year ago

Looks like you are on Mac. So, to compile packages from source you need XCode from Apple and the command line tools that go with it. But you can also download the binary pre-compiled version of the package by answering "no" to the question "Do you want to install from sources the package which needs compilation?". And you can also use install.packages("ade4", type="binary"), see ?install.packages

melodyoungg commented 1 year ago

Hi, I downloaded the XCode and command line tools. These are the errors:

install.packages("ade4")

There is a binary version available but the source version is later: binary source needs_compilation ade4 1.7-20 1.7-22 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes installing the source package ‘ade4’

trying URL 'https://cran.rstudio.com/src/contrib/ade4_1.7-22.tar.gz' Content type 'application/x-gzip' length 3365194 bytes (3.2 MB)

downloaded 3.2 MB

Best regards,

Melody Young GS2

On Mon, Feb 6, 2023 at 1:14 PM Jean Thioulouse @.***> wrote:

Looks like you are on Mac. So, to compile packages from source you need XCode from Apple and the command line tools that go with it. But you can also download the binary pre-compiled version of the package by answering "no" to the question "Do you want to install from sources the package which needs compilation?". And you can also use install.packages("ade4", type="binary"), see ?install.packages

— Reply to this email directly, view it on GitHub https://github.com/sdray/ade4/issues/32#issuecomment-1419538788, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5Q3QYIMA74VLGBOC2PM6RTWWE5Q5ANCNFSM6AAAAAAUS7OERQ . You are receiving this because you authored the thread.Message ID: @.***>

melodyoungg commented 1 year ago

I also tried your code:

install.packages("ade4", type="binary")

There is a binary version available (and will be installed) but the source version is later: binary source ade4 1.7-20 1.7-22

trying URL ' https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ade4_1.7-20.tgz ' Content type 'application/x-gzip' length 5483299 bytes (5.2 MB)

downloaded 5.2 MB

The downloaded binary packages are in /var/folders/88/_w7_f_l52yn8b3pm69tlz9th0000gp/T//RtmputPURe/downloaded_packages

libary(ade4) Error in libary(ade4) : could not find function "libary" library(ade4) Error: package or namespace load failed for ‘ade4’ in get(Info[i, 1], envir = env): lazy-load database '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4/R/ade4.rdb' is corrupt In addition: Warning message: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1

Best regards,

Melody Young GS2

On Mon, Feb 6, 2023 at 1:22 PM Melody Young @.***> wrote:

Hi, I downloaded the XCode and command line tools. These are the errors:

install.packages("ade4")

There is a binary version available but the source version is later: binary source needs_compilation ade4 1.7-20 1.7-22 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes installing the source package ‘ade4’

trying URL 'https://cran.rstudio.com/src/contrib/ade4_1.7-22.tar.gz' Content type 'application/x-gzip' length 3365194 bytes (3.2 MB)

downloaded 3.2 MB

  • installing source package ‘ade4’ ... package ‘ade4’ successfully unpacked and MD5 sums checked using staged installation ** libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ade4libCpp.cpp -o ade4libCpp.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c adesub.c -o adesub.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c divsub.c -o divsub.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fourthcorner.c -o fourthcorner.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phylog.c -o phylog.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testamova.c -o testamova.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testdim.c -o testdim.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testrlq.c -o testrlq.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tests.c -o tests.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testsCpp.cpp -o testsCpp.o clang++ -arch arm64 -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/opt/R/arm64/lib -o ade4.so RcppExports.o ade4libCpp.o adesub.o divsub.o fourthcorner.o init.o phylog.o testamova.o testdim.o testrlq.o tests.o testsCpp.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [ade4.so] Error 1 ERROR: compilation failed for package ‘ade4’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4’
  • restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4’ Warning in install.packages : installation of package ‘ade4’ had non-zero exit status

Best regards,

Melody Young GS2

On Mon, Feb 6, 2023 at 1:14 PM Jean Thioulouse @.***> wrote:

Looks like you are on Mac. So, to compile packages from source you need XCode from Apple and the command line tools that go with it. But you can also download the binary pre-compiled version of the package by answering "no" to the question "Do you want to install from sources the package which needs compilation?". And you can also use install.packages("ade4", type="binary"), see ?install.packages

— Reply to this email directly, view it on GitHub https://github.com/sdray/ade4/issues/32#issuecomment-1419538788, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5Q3QYIMA74VLGBOC2PM6RTWWE5Q5ANCNFSM6AAAAAAUS7OERQ . You are receiving this because you authored the thread.Message ID: @.***>

melodyoungg commented 1 year ago

I shut down R and reran install.packages("ade4", type="binary") and it seemed to work. Thank you for your help.

Best regards,

Melody Young GS2

On Mon, Feb 6, 2023 at 1:24 PM Melody Young @.***> wrote:

I also tried your code:

install.packages("ade4", type="binary")

There is a binary version available (and will be installed) but the source version is later: binary source ade4 1.7-20 1.7-22

trying URL ' https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ade4_1.7-20.tgz ' Content type 'application/x-gzip' length 5483299 bytes (5.2 MB)

downloaded 5.2 MB

The downloaded binary packages are in

/var/folders/88/_w7_f_l52yn8b3pm69tlz9th0000gp/T//RtmputPURe/downloaded_packages

libary(ade4) Error in libary(ade4) : could not find function "libary" library(ade4) Error: package or namespace load failed for ‘ade4’ in get(Info[i, 1], envir = env): lazy-load database '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4/R/ade4.rdb' is corrupt In addition: Warning message: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1

Best regards,

Melody Young GS2

On Mon, Feb 6, 2023 at 1:22 PM Melody Young @.***> wrote:

Hi, I downloaded the XCode and command line tools. These are the errors:

install.packages("ade4")

There is a binary version available but the source version is later: binary source needs_compilation ade4 1.7-20 1.7-22 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes installing the source package ‘ade4’

trying URL 'https://cran.rstudio.com/src/contrib/ade4_1.7-22.tar.gz' Content type 'application/x-gzip' length 3365194 bytes (3.2 MB)

downloaded 3.2 MB

  • installing source package ‘ade4’ ... package ‘ade4’ successfully unpacked and MD5 sums checked using staged installation ** libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ade4libCpp.cpp -o ade4libCpp.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c adesub.c -o adesub.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c divsub.c -o divsub.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fourthcorner.c -o fourthcorner.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phylog.c -o phylog.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testamova.c -o testamova.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testdim.c -o testdim.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testrlq.c -o testrlq.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tests.c -o tests.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c testsCpp.cpp -o testsCpp.o clang++ -arch arm64 -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/opt/R/arm64/lib -o ade4.so RcppExports.o ade4libCpp.o adesub.o divsub.o fourthcorner.o init.o phylog.o testamova.o testdim.o testrlq.o tests.o testsCpp.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [ade4.so] Error 1 ERROR: compilation failed for package ‘ade4’
  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4’
  • restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4’ Warning in install.packages : installation of package ‘ade4’ had non-zero exit status

Best regards,

Melody Young GS2

On Mon, Feb 6, 2023 at 1:14 PM Jean Thioulouse @.***> wrote:

Looks like you are on Mac. So, to compile packages from source you need XCode from Apple and the command line tools that go with it. But you can also download the binary pre-compiled version of the package by answering "no" to the question "Do you want to install from sources the package which needs compilation?". And you can also use install.packages("ade4", type="binary"), see ?install.packages

— Reply to this email directly, view it on GitHub https://github.com/sdray/ade4/issues/32#issuecomment-1419538788, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5Q3QYIMA74VLGBOC2PM6RTWWE5Q5ANCNFSM6AAAAAAUS7OERQ . You are receiving this because you authored the thread.Message ID: @.***>

thioulouse commented 1 year ago

warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' ld: library not found for -lgfortran

Yes indeed, you also need to install a Fortran compiler. This is explained on the Mac dev tools page: https://cran.univ-lyon1.fr/CRAN/bin/macosx/tools

thioulouse commented 1 year ago

Also note that if you need the development version of ade4 (1.7-22) you can use install.packages("http://pbil.univ-lyon1.fr/members/thioulouse/bin/macosx/macosxarm/ade4_1.7-22.tgz") if you are on a Mac with an arm (Apple M series) processor, or install.packages("http://pbil.univ-lyon1.fr/members/thioulouse/bin/macosx/macosx/ade4_1.7-22.tgz") if you are on a Mac with an Intel processor.

emphillips18 commented 1 year ago

I shut down R and reran install.packages("ade4", type="binary") and it seemed to work. Thank you for your help. Best regards, Melody Young GS2 … On Mon, Feb 6, 2023 at 1:24 PM Melody Young @.> wrote: I also tried your code: install.packages("ade4", type="binary") There is a binary version available (and will be installed) but the source version is later: binary source ade4 1.7-20 1.7-22 trying URL ' https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.2/ade4_1.7-20.tgz ' Content type 'application/x-gzip' length 5483299 bytes (5.2 MB) ================================================== downloaded 5.2 MB The downloaded binary packages are in /var/folders/88/_w7_f_l52yn8b3pm69tlz9th0000gp/T//RtmputPURe/downloaded_packages > libary(ade4) Error in libary(ade4) : could not find function "libary" > library(ade4) Error: package or namespace load failed for ‘ade4’ in get(Info[i, 1], envir = env): lazy-load database '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4/R/ade4.rdb' is corrupt In addition: Warning message: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 Best regards, Melody Young GS2 On Mon, Feb 6, 2023 at 1:22 PM Melody Young @.> wrote: > Hi, I downloaded the XCode and command line tools. These are the errors: > > install.packages("ade4") > > There is a binary version available but the source version is later: > binary source needs_compilation > ade4 1.7-20 1.7-22 TRUE > > Do you want to install from sources the package which needs compilation? > (Yes/no/cancel) yes > installing the source package ‘ade4’ > > trying URL 'https://cran.rstudio.com/src/contrib/ade4_1.7-22.tar.gz' > Content type 'application/x-gzip' length 3365194 bytes (3.2 MB) > ================================================== > downloaded 3.2 MB > > installing source package ‘ade4’ ... > package ‘ade4’ successfully unpacked and MD5 sums checked > using staged installation > libs > clang++ -arch arm64 -std=gnu++14 > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > RcppExports.cpp -o RcppExports.o > clang++ -arch arm64 -std=gnu++14 > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > ade4libCpp.cpp -o ade4libCpp.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > adesub.c -o adesub.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > divsub.c -o divsub.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > fourthcorner.c -o fourthcorner.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > init.c -o init.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > phylog.c -o phylog.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > testamova.c -o testamova.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > testdim.c -o testdim.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > testrlq.c -o testrlq.o > clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" > -DNDEBUG -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > tests.c -o tests.o > clang++ -arch arm64 -std=gnu++14 > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > -I../inst/include > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' > -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/RcppArmadillo/include' > -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c > testsCpp.cpp -o testsCpp.o > clang++ -arch arm64 -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/opt/R/arm64/lib -o ade4.so RcppExports.o ade4libCpp.o adesub.o divsub.o > fourthcorner.o init.o phylog.o testamova.o testdim.o testrlq.o tests.o > testsCpp.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack > -L/Library/Frameworks/R.framework/Resources/lib -lRblas > -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 > -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework > -Wl,CoreFoundation > ld: warning: directory not found for option > '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' > ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib' > ld: library not found for -lgfortran > clang: error: linker command failed with exit code 1 (use -v to see > invocation) > make: [ade4.so] Error 1 > ERROR: compilation failed for package ‘ade4’ > removing > ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4’ > restoring previous > ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ade4’ > Warning in install.packages : > installation of package ‘ade4’ had non-zero exit status > > Best regards, > > Melody Young > GS2 > > > > On Mon, Feb 6, 2023 at 1:14 PM Jean Thioulouse @.> > wrote: > >> Looks like you are on Mac. So, to compile packages from source you need >> XCode from Apple and the command line tools that go with it. But you can >> also download the binary pre-compiled version of the package by answering >> "no" to the question "Do you want to install from sources the package which >> needs compilation?". And you can also use install.packages("ade4", >> type="binary"), see ?install.packages >> >> — >> Reply to this email directly, view it on GitHub >> <#32 (comment)>, or >> unsubscribe >> https://github.com/notifications/unsubscribe-auth/A5Q3QYIMA74VLGBOC2PM6RTWWE5Q5ANCNFSM6AAAAAAUS7OERQ >> . >> You are receiving this because you authored the thread.Message ID: >> @.> >> >

I also had this issue (on a Mac), but I used install.packages("ade4", type="binary") and it worked. Thank you!