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dorianps / LESYMAP

Lesion to Symptom Mapping in R
https://dorianps.github.io/LESYMAP/
Apache License 2.0
32 stars 11 forks source link

Installation issues (R Studio 2023.03.0; R 4.0.4) #37

Open nicolettabiondo opened 1 year ago

nicolettabiondo commented 1 year ago

Hi,

I'm trying to install LESYMAP on R Studio (2023.03.0, R 4.0.4) but I get an error from the very beginning (see below). My understanding is that the issue starts here "Error in cmaker::cmake() : cmake command not found".

I've tried to look for a R package called "cmaker" but I couldn't find it. I've also tried to install CMake for Windows (not sure this actually helps) but nothing.

A note (which might be relevant): RStudio asks me to update many packages. I tried both ways (updating the packages as recommended, not updating anything) and the installation fails anyways.

Any suggestions? Thanks a lot!

Error:

./configure.win: line 73: -G: command not found ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture

"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.4/include" -DNDEBUG -I'C:/Users/nicol/Documents/R/win-library/4.0/Rcpp/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dummy.cpp -o dummy.o cd itkb && mingw32-make -j 2 || \ mingw32-make install || \ /usr/bin/make VERBOSE=1 -j 2 || \ /usr/bin/make install && ls ../ && rm -rf ../itks && \ rm -rf ITKInternalEigen3-build/Makefile && \ rm -rf CMakeFiles/ && rm -rf Modules/ && rm -rf CMakeTmp/ && \ rm -f Makefile && \ rm -rf Utilities/Doxygen sh: line 1: mingw32-make: command not found sh: line 2: mingw32-make: command not found make[1]: Entering directory '/c/Users/nicol/AppData/Local/Temp/RtmpcDGhs4/R.INSTALL2b30699fef5/ITKR/src/itkb' make[1]: No targets specified and no makefile found. Stop. make[1]: Leaving directory '/c/Users/nicol/AppData/Local/Temp/RtmpcDGhs4/R.INSTALL2b30699fef5/ITKR/src/itkb' make[1]: Entering directory '/c/Users/nicol/AppData/Local/Temp/RtmpcDGhs4/R.INSTALL2b30699fef5/ITKR/src/itkb' make[1]: No rule to make target 'install'. Stop. make[1]: Leaving directory '/c/Users/nicol/AppData/Local/Temp/RtmpcDGhs4/R.INSTALL2b30699fef5/ITKR/src/itkb' make: *** [Makevars.win:13: libs] Error 2 ERROR: compilation failed for package 'ITKR'

dorianps commented 1 year ago

You can't install on Windows. Lesymap works on Linux or Mac, not windows. Sorry

On Sun, Apr 23, 2023, 4:36 AM nicolettabiondo @.***> wrote:

Hi,

I'm trying to install LESYMAP on R Studio (2023.03.0, R 4.0.4) but I get an error from the very beginning (see below). My understanding is that the issue starts here "Error in cmaker::cmake() : cmake command not found".

I've tried to look for a R package called "cmaker" but I couldn't find it. I've also tried to install CMake for Windows (not sure this actually helps) but nothing.

A note (which might be relevant): RStudio asks me to update many packages. I tried both ways (updating the packages as recommended, not updating anything) and the installation fails anyways.

Any suggestions? Thanks a lot!

Error:

  • installing source package 'ITKR' ... ** using non-staged installation via StagedInstall field Loading required namespace: git2r cloning into './itks'... Receiving objects: 1% (5359/535851), 2481 kb Receiving objects: 11% (58944/535851), 20548 kb Receiving objects: 21% (112529/535851), 65094 kb Receiving objects: 31% (166114/535851), 96240 kb Receiving objects: 41% (219699/535851), 122936 kb Receiving objects: 51% (273285/535851), 149288 kb Receiving objects: 61% (326870/535851), 164321 kb Receiving objects: 71% (380455/535851), 175599 kb Receiving objects: 81% (434040/535851), 180314 kb Receiving objects: 91% (487625/535851), 185245 kb Receiving objects: 100% (535851/535851), 196820 kb, done. Error in cmaker::cmake() : cmake command not found Execution halted

./configure.win: line 73: -G: command not found ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture

"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA1/R/R-401.4/include" -DNDEBUG -I'C:/Users/nicol/Documents/R/win-library/4.0/Rcpp/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dummy.cpp -o dummy.o cd itkb && mingw32-make -j 2 || mingw32-make install || /usr/bin/make VERBOSE=1 -j 2 || /usr/bin/make install && ls ../ && rm -rf ../itks && rm -rf ITKInternalEigen3-build/Makefile && rm -rf CMakeFiles/ && rm -rf Modules/ && rm -rf CMakeTmp/ && rm -f Makefile && rm -rf Utilities/Doxygen sh: line 1: mingw32-make: command not found sh: line 2: mingw32-make: command not found make[1]: Entering directory '/c/Users/nicol/AppData/Local/Temp/RtmpcDGhs4/R.INSTALL2b30699fef5/ITKR/src/itkb' make[1]: No targets specified and no makefile found. Stop. make[1]: Leaving directory '/c/Users/nicol/AppData/Local/Temp/RtmpcDGhs4/R.INSTALL2b30699fef5/ITKR/src/itkb' make[1]: Entering directory '/c/Users/nicol/AppData/Local/Temp/RtmpcDGhs4/R.INSTALL2b30699fef5/ITKR/src/itkb' make[1]: No rule to make target 'install'. Stop. make[1]: Leaving directory '/c/Users/nicol/AppData/Local/Temp/RtmpcDGhs4/R.INSTALL2b30699fef5/ITKR/src/itkb' make: *** [Makevars.win:13: libs] Error 2 ERROR: compilation failed for package 'ITKR'

  • removing 'C:/Users/nicol/Documents/R/win-library/4.0/ITKR'

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nicolettabiondo commented 1 year ago

Hi! Thanks. I didn't know I couldn't use it on Windows.

A colleague of mine tried to install the package on a Mac (RStudio 2022.07.2; R 4.2.2). I attach below the output and the errors she got (she also tried to skip the package updates and ran into an error too):

install.packages("devtools", repos = "http://cloud.r-project.org/") trying URL 'http://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz' Content type 'application/x-gzip' length 421790 bytes (411 KB)

downloaded 411 KB

The downloaded binary packages are in /var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T//RtmpVhTfWv/downloaded_packages

devtools::install_github('dorianps/LESYMAP') Downloading GitHub repo dorianps/LESYMAP@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: RcppArmad... (0.11.4.2.1 -> 0.12.2.0.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 ANTsR (NA -> 14996a710...) [GitHub] ANTsRCore (NA -> 24dbfc897...) [GitHub] RcppArmad... (0.11.4.2.1 -> 0.12.2.0.0 ) [CRAN] Downloading GitHub repo ANTsX/ANTsR@HEAD Downloading GitHub repo stnava/ITKR@HEAD ✔ checking for file ‘/private/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T/RtmpVhTfWv/remotesd2dc1d3d3782/stnava-ITKR-01d69c4/DESCRIPTION’ ... ─ preparing ‘ITKR’: ✔ 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 ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘ITKR_0.6.0.0.2.tar.gz’

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example:

git switch -c

Or undo this operation with:

git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 73e883daba Merge pull request #3481 from thewtex/53rc4-content-link CMake Error at CMakeLists.txt:15 (cmake_minimum_required): CMake 3.16.3...3.19.7 or higher is required. You are running version 3.11.4

-- Configuring incomplete, errors occurred! libs clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dummy.cpp -o dummy.o cd itkb && make -j 2 && make install && rm -rf ../itks \ && rm -rf CMakeFiles/ && rm -rf Modules/ && rm -rf CMakeTmp/ \ rm -f Makefile && rm -rf Utilities/Doxygen make[1]: ** No targets specified and no makefile found. Stop. make: [libs] Error 2 ERROR: compilation failed for package ‘ITKR’

ERROR: dependency ‘ITKR’ is not available for package ‘ANTsRCore’

ERROR: dependencies ‘ANTsRCore’, ‘ITKR’ are not available for package ‘ANTsR’

The downloaded binary packages are in /var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T//RtmpVhTfWv/downloaded_packages Downloading GitHub repo ANTsX/ANTsR@HEAD Skipping ANTsR, it is already being installed Downloading GitHub repo ANTsX/ANTsRCore@HEAD Skipping ANTsRCore, it is already being installed ✔ checking for file ‘/private/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T/RtmpVhTfWv/remotesd2dc37b58212/dorianps-LESYMAP-cd13aa0/DESCRIPTION’ ... ─ preparing ‘LESYMAP’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories Omitted ‘LazyData’ from DESCRIPTION ─ building ‘LESYMAP_0.0.0.9221.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘LESYMAP/inst/extdata/template/other_templates/MNI152_2009c/mni_icbm152_t1_tal_nlin_sym_09c_mask.nii.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘LESYMAP/inst/extdata/template/other_templates/MNI152_2009c/mni_icbm152_t1_tal_nlin_sym_09c_mask_skullnoface.nii.gz’

ERROR: dependencies ‘ANTsR’, ‘ANTsRCore’ are not available for package ‘LESYMAP’

dorianps commented 1 year ago

Can you please check the ANTsR GitHub page for Mac requirements. Some compilers and ccmake may be needed to install on the computer. Sorry for not being of more help but the upstream packages have their own help. In alternative, you could use docker container versions I have published. Check my GitHub docker page.

On Sat, Apr 29, 2023, 1:12 AM nicolettabiondo @.***> wrote:

Hi! Thanks. I didn't know I couldn't use it on Windows.

A colleague of mine tried to install the package on a Mac (RStudio 2022.07.2; R 4.2.2). I attach below the output and the errors she got (she also tried to skip the package updates and ran into an error too):

install.packages("devtools", repos = "http://cloud.r-project.org/") trying URL ' http://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/devtools_2.4.5.tgz ' Content type 'application/x-gzip' length 421790 bytes (411 KB)

downloaded 411 KB

The downloaded binary packages are in

/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T//RtmpVhTfWv/downloaded_packages

devtools::install_github('dorianps/LESYMAP') Downloading GitHub repo @.*** These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All 2: CRAN packages only 3: None 4: RcppArmad... (0.11.4.2.1 -> 0.12.2.0.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 ANTsR (NA -> 14996a710...) [GitHub] ANTsRCore (NA -> 24dbfc897...) [GitHub] RcppArmad... (0.11.4.2.1 -> 0.12.2.0.0 ) [CRAN] Downloading GitHub repo @. Downloading GitHub repo @. ✔ checking for file ‘/private/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T/RtmpVhTfWv/remotesd2dc1d3d3782/stnava-ITKR-01d69c4/DESCRIPTION’ ... ─ preparing ‘ITKR’: ✔ 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 ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘ITKR_0.6.0.0.2.tar.gz’

  • installing source package ‘ITKR’ ... ** using non-staged installation via StagedInstall field Cloning into 'itks'... Updating files: 100% (16536/16536), done. Already on 'master' Your branch is up to date with 'origin/master'. Note: switching to 'v5.3rc04'.

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example:

git switch -c

Or undo this operation with:

git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 73e883daba Merge pull request #3481 from thewtex/53rc4-content-link CMake Error at CMakeLists.txt:15 (cmake_minimum_required): CMake 3.16.3...3.19.7 or higher is required. You are running version 3.11.4

-- Configuring incomplete, errors occurred! libs clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dummy.cpp -o dummy.o cd itkb && make -j 2 && make install && rm -rf ../itks && rm -rf CMakeFiles/ && rm -rf Modules/ && rm -rf CMakeTmp/ rm -f Makefile && rm -rf Utilities/Doxygen make[1]: ** No targets specified and no makefile found. Stop. make: [libs] Error 2 ERROR: compilation failed for package ‘ITKR’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ITKR’ Downloading GitHub repo @. Downloading GitHub repo @. Skipping ITKR, it is already being installed Downloading GitHub repo @.*** Skipping ITKR, it is already being installed ✔ checking for file ‘/private/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T/RtmpVhTfWv/remotesd2dc205a5104/ANTsX-ANTsRCore-24dbfc8/DESCRIPTION’ ... ─ preparing ‘ANTsRCore’: ✔ 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 ‘ANTsRCore_0.7.5.tar.gz’

ERROR: dependency ‘ITKR’ is not available for package ‘ANTsRCore’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/ANTsRCore’ Downloading GitHub repo @. Skipping ITKR, it is already being installed Downloading GitHub repo @. Skipping ANTsRCore, it is already being installed ✔ checking for file ‘/private/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T/RtmpVhTfWv/remotesd2dc272fa23e/ANTsX-ANTsR-14996a7/DESCRIPTION’ ... ─ preparing ‘ANTsR’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts (408ms) ─ checking for empty or unneeded directories ─ building ‘ANTsR_0.5.7.5.tar.gz’

ERROR: dependencies ‘ANTsRCore’, ‘ITKR’ are not available for package ‘ANTsR’

The downloaded binary packages are in

/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T//RtmpVhTfWv/downloaded_packages Downloading GitHub repo @. Skipping ANTsR, it is already being installed Downloading GitHub repo @. Skipping ANTsRCore, it is already being installed ✔ checking for file ‘/private/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T/RtmpVhTfWv/remotesd2dc37b58212/dorianps-LESYMAP-cd13aa0/DESCRIPTION’ ... ─ preparing ‘LESYMAP’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories Omitted ‘LazyData’ from DESCRIPTION ─ building ‘LESYMAP_0.0.0.9221.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘LESYMAP/inst/extdata/template/other_templates/MNI152_2009c/mni_icbm152_t1_tal_nlin_sym_09c_mask.nii.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

‘LESYMAP/inst/extdata/template/other_templates/MNI152_2009c/mni_icbm152_t1_tal_nlin_sym_09c_mask_skullnoface.nii.gz’

ERROR: dependencies ‘ANTsR’, ‘ANTsRCore’ are not available for package ‘LESYMAP’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/LESYMAP’ Warning messages: 1: In i.p(...) : installation of package ‘/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T//RtmpVhTfWv/filed2dc1e0746cd/ITKR_0.6.0.0.2.tar.gz’ had non-zero exit status 2: In i.p(...) : installation of package ‘/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T//RtmpVhTfWv/filed2dc614915e2/ANTsRCore_0.7.5.tar.gz’ had non-zero exit status 3: In i.p(...) : installation of package ‘/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T//RtmpVhTfWv/filed2dc3e3aec78/ANTsR_0.5.7.5.tar.gz’ had non-zero exit status 4: In i.p(...) : installation of package ‘/var/folders/5f/t5zwmnj56gn791gxfxjnz3s00000gn/T//RtmpVhTfWv/filed2dc71dff99c/LESYMAP_0.0.0.9221.tar.gz’ had non-zero exit status

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