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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
127 stars 35 forks source link

Installing issue - OS Catalina 10.15.7 #330

Closed Georgina85 closed 3 years ago

Georgina85 commented 3 years ago

Hello, I am trying to install LESYMAP. I use OS Catalina 10.15.7 and I am having the following issue when trying to install ANTsR:

(converted from warning) installation of package ‘/var/folders/96/xd970zqj45xcq6zzyccv0jrw0000gn/T//RtmpuACDzr/filee1333d67fed8/ANTsRCore_0.7.4.8.tar.gz’ had non-zero exit status

Could someone help me to resolve it? Thank you in advance, Georgina

jefferis commented 3 years ago

Hello @Georgina85, I'm just a user, not a dev, but I'm afraid you'll need to provide some more detailed error messages to help them debug that install issue. Best, Greg.

Georgina85 commented 3 years ago

Hello @jefferis, thank you for your reply. This is the full error, I don't know if it is more helpful:

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 5b7c090b BUG: revert last change - just build a function directly in R -- The C compiler identification is AppleClang 11.0.3.11030032 -- The CXX compiler identification is AppleClang 11.0.3.11030032 -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Not using CCache -- Performing Test C_HAS_WARNING-Wno-uninitialized -- Performing Test C_HAS_WARNING-Wno-uninitialized - Success -- Performing Test C_HAS_WARNING-Wno-unused-parameter -- Performing Test C_HAS_WARNING-Wno-unused-parameter - Success -- Performing Test C_HAS_WARNING-Wall -- Performing Test C_HAS_WARNING-Wall - Success -- Performing Test C_HAS_WARNING-Wno-long-double -- Performing Test C_HAS_WARNING-Wno-long-double - Failed -- Performing Test C_HAS_WARNING-Wcast-align -- Performing Test C_HAS_WARNING-Wcast-align - Success -- Performing Test C_HAS_WARNING-Wdisabled-optimization -- Performing Test C_HAS_WARNING-Wdisabled-optimization - Success -- Performing Test C_HAS_WARNING-Wextra -- Performing Test C_HAS_WARNING-Wextra - Success -- Performing Test C_HAS_WARNING-Wformat_2 -- Performing Test C_HAS_WARNING-Wformat_2 - Success -- Performing Test C_HAS_WARNING-Winvalid-pch -- Performing Test C_HAS_WARNING-Winvalid-pch - Success -- Performing Test C_HAS_WARNING-Wno-format-nonliteral -- Performing Test C_HAS_WARNING-Wno-format-nonliteral - Success -- Performing Test C_HAS_WARNING-Wpointer-arith -- Performing Test C_HAS_WARNING-Wpointer-arith - Success -- Performing Test C_HAS_WARNING-Wshadow -- Performing Test C_HAS_WARNING-Wshadow - Success -- Performing Test C_HAS_WARNING-Wunused -- Performing Test C_HAS_WARNING-Wunused - Success -- Performing Test C_HAS_WARNING-Wwrite-strings -- Performing Test C_HAS_WARNING-Wwrite-strings - Success -- Performing Test C_HAS_WARNING-funit-at-a-time -- Performing Test C_HAS_WARNING-funit-at-a-time - Success -- Performing Test C_HAS_WARNING-Wno-strict-overflow -- Performing Test C_HAS_WARNING-Wno-strict-overflow - Success -- Performing Test CXX_HAS_WARNING-Wall -- Performing Test CXX_HAS_WARNING-Wall - Success -- Performing Test CXX_HAS_WARNING-Wno-long-double -- Performing Test CXX_HAS_WARNING-Wno-long-double - Failed -- Performing Test CXX_HAS_WARNING-Wcast-align -- Performing Test CXX_HAS_WARNING-Wcast-align - Success -- Performing Test CXX_HAS_WARNING-Wdisabled-optimization -- Performing Test CXX_HAS_WARNING-Wdisabled-optimization - Success -- Performing Test CXX_HAS_WARNING-Wextra -- Performing Test CXX_HAS_WARNING-Wextra - Success -- Performing Test CXX_HAS_WARNING-Wformat_2 -- Performing Test CXX_HAS_WARNING-Wformat_2 - Success -- Performing Test CXX_HAS_WARNING-Winvalid-pch -- Performing Test CXX_HAS_WARNING-Winvalid-pch - Success -- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral -- Performing Test CXX_HAS_WARNING-Wno-format-nonliteral - Success -- Performing Test CXX_HAS_WARNING-Wpointer-arith -- Performing Test CXX_HAS_WARNING-Wpointer-arith - Success -- Performing Test CXX_HAS_WARNING-Wshadow -- Performing Test CXX_HAS_WARNING-Wshadow - Success -- Performing Test CXX_HAS_WARNING-Wunused -- Performing Test CXX_HAS_WARNING-Wunused - Success -- Performing Test CXX_HAS_WARNING-Wwrite-strings -- Performing Test CXX_HAS_WARNING-Wwrite-strings - Success -- Performing Test CXX_HAS_WARNING-funit-at-a-time -- Performing Test CXX_HAS_WARNING-funit-at-a-time - Success -- Performing Test CXX_HAS_WARNING-Wno-strict-overflow -- Performing Test CXX_HAS_WARNING-Wno-strict-overflow - Success -- Performing Test CXX_HAS_WARNING-Wno-deprecated -- Performing Test CXX_HAS_WARNING-Wno-deprecated - Success -- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof -- Performing Test CXX_HAS_WARNING-Wno-invalid-offsetof - Success -- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template -- Performing Test CXX_HAS_WARNING-Wno-undefined-var-template - Success -- Performing Test CXX_HAS_WARNING-Woverloaded-virtual -- Performing Test CXX_HAS_WARNING-Woverloaded-virtual - Success -- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel -- Performing Test CXX_HAS_WARNING-Wstrict-null-sentinel - Failed -- Performing Test C_HAS_WARNING-mtune_native -- Performing Test C_HAS_WARNING-mtune_native - Success -- Performing Test C_HAS_WARNING-march_corei7 -- Performing Test C_HAS_WARNING-march_corei7 - Success -- Performing Test CXX_HAS_WARNING-mtune_native -- Performing Test CXX_HAS_WARNING-mtune_native - Success -- Performing Test CXX_HAS_WARNING-march_corei7 -- Performing Test CXX_HAS_WARNING-march_corei7 - Success -- Found Git: /usr/bin/git (found version "2.24.1 (Apple Git-126)") -- SuperBuild - ANTS => Requires ITKv5, -- SuperBuild - ITKv5[OK] -- SuperBuild - ANTS[OK] -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project:

COPY_SCRIPT_FILES_TO_BIN_DIR

-- Build files have been written to: /private/var/folders/96/xd970zqj45xcq6zzyccv0jrw0000gn/T/RtmpBxxBLi/R.INSTALLe731111b1dc1/ANTsRCore/src/antb ** libs /Users/georgina/.R/Makevars:2: *** missing separator. Stop. ERROR: compilation failed for package ‘ANTsRCore’

jefferis commented 3 years ago

it looks like there is an error in this file on your system which modifies R's compilation behaviour:

/Users/georgina/.R/Makevars:2: *** missing separator. Stop.

which is actually not part of of ANTsR. If you are not sure of the problem you could share it here. For example in terminal

cat /Users/georgina/.R/Makevars
Georgina85 commented 3 years ago

Thanks again for your help! Does that help: georgina$ cat /Users/georgina/.R/Makevars FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 - L/usr/local/gfortran/lib -lgfortran -lquadmath -lm

cookpa commented 3 years ago

What was the install command?

Georgina85 commented 3 years ago

library(devtools) ?install_github devtools::session_info() devtools::install_github('dorianps/LESYMAP')

The RStudio version is 1.3.1073

jefferis commented 3 years ago

Is this one line or two ?

FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -
L/usr/local/gfortran/lib -lgfortran -lquadmath -lm

I assume it should be one line (with a blank line following for pref)

Georgina85 commented 3 years ago

Actually it is two lines.

jefferis commented 3 years ago

Actually it is two lines.

So you need to edit it to make it one.

cookpa commented 3 years ago

Good call @jefferis

Georgina85 commented 3 years ago

Thank you both for your replies, but I am kind of confused. The aforementioned command is the output when I typed cat /Users/georgina/.R/Makevars. When you suggest to edit it, you mean to run it as one command at the terminal?

jefferis commented 3 years ago

open -e /Users/georgina/.R/Makevars

to edit and fix

cookpa commented 3 years ago

Or from the command line

echo 'FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm' > ~/.R/Makevars

There should be no line breaks in the above.

If this doesn't fix it, you might need other variables defined for Catalina. I'll find the other issue

cookpa commented 3 years ago

Here's the Makevars file I'm using

https://github.com/ANTsX/ANTsR/issues/291#issuecomment-564825846

cookpa commented 3 years ago

However I should add I've installed ANTsR on another machine with 10.15.6 without any problems, without doing anything to Makevars. I just installed XCode, then devtools, then ANTsR.

Georgina85 commented 3 years ago

I have just corrected the script and installation was successful! @jefferis and @cookpa thank you once again for your time and help!!!

cookpa commented 3 years ago

Excellent, thanks for the update.