Closed Georgina85 closed 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.
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’
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
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
What was the install command?
library(devtools) ?install_github devtools::session_info() devtools::install_github('dorianps/LESYMAP')
The RStudio version is 1.3.1073
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)
Actually it is two lines.
Actually it is two lines.
So you need to edit it to make it one.
Good call @jefferis
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?
open -e /Users/georgina/.R/Makevars
to edit and fix
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
Here's the Makevars file I'm using
https://github.com/ANTsX/ANTsR/issues/291#issuecomment-564825846
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.
I have just corrected the script and installation was successful! @jefferis and @cookpa thank you once again for your time and help!!!
Excellent, thanks for the update.
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