leidenbase compilation failed Mac OS X #6

Connorr0 · 2019-09-26T17:07:08Z

Hello, I am getting the following error when I try to install leidenbase:

ld: file not found: /usr/lib/system/libsystem_symptoms.dylib for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [leidenbase.so] Error 1
ERROR: compilation failed for package ‘leidenbase’

removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/leidenbase’

I was wondering if you have any advice?

Connorr0 · 2019-09-26T17:53:16Z

I did some digging and it looks like this error might be be because I am using OS X 10.11. Does this build work on upgraded Mac OS?

brgew · 2019-09-26T22:17:56Z

Hi @Connorr0,

I test leidenbase on a MacBook Pro running OS X version 10.11.6, and it builds and runs. I used the R package distributed by CRAN, which is at the URL

https://cran.r-project.org/bin/macosx/R-3.6.1.pkg

and I installed the CRAN gfortran compiler, which is at the URL

https://cran.r-project.org/bin/macosx/tools/gfortran-6.1.pkg

I searched using google for information about the error that you report and found evidence that R builds using the brew command on OS X 10.11 can fail because there is no
libsystem_symptoms.dylib library, as you noted. I have not tried using brew to build R on a more recent MacOS version so I cannot comment on your most recent question. Is there a reason to avoid upgrading to a more recent MacOS version?

mjdufort · 2019-09-27T20:28:23Z

I was running into a slightly different error with compilation of leidenbase (a different file not found), on Mac OS X 10.14.6 and R 3.5.2. I had initially installed gfortran using homebrew, and that was not working. After I installed the CRAN gfortran compiler, linked above by brgew, the compilation and install of leidenbase worked fine.

Connorr0 · 2019-09-30T16:56:11Z

I reinstalled gofortran (from the link above) and restarted my computer and now received the following error:

installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘leidenbase’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so, 6): Library not loaded: @rpath/libxml2.2.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so
  Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:
  (converted from warning) installation of package ‘/var/folders/s3/g0t_3241673fm58w53j69d6w0000gn/T//Rtmpi7qSCs/file26c23bc25b3/leidenbase_0.1.0.tar.gz’ had non-zero exit status

I also get a lot of output printed to terminal. Here are the first few lines:

gfortran  -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd.f -o cigraph/src/AMD/Source/amd.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
Warning: Nonconforming tab character in column 1 of line 422
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_1.c -o cigraph/src/AMD/Source/amd_1.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_2.c -o cigraph/src/AMD/Source/amd_2.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_aat.c -o cigraph/src/AMD/Source/amd_aat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_control.c -o cigraph/src/AMD/Source/amd_control.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_defaults.c -o cigraph/src/AMD/Source/amd_defaults.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_dump.c -o cigraph/src/AMD/Source/amd_dump.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_global.c -o cigraph/src/AMD/Source/amd_global.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_info.c -o cigraph/src/AMD/Source/amd_info.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_order.c -o cigraph/src/AMD/Source/amd_order.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_post_tree.c -o cigraph/src/AMD/Source/amd_post_tree.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_postorder.c -o cigraph/src/AMD/Source/amd_postorder.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_preprocess.c -o cigraph/src/AMD/Source/amd_preprocess.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -Icigraph/src -Icigraph/include -Icigraph/src/cs -Icigraph/src/glpk -Icigraph/src/plfit -Icigraph/src/CHOLMOD/Include -Icigraph/src/AMD/Include -Icigraph/src/COLAMD/Include -Icigraph/src/SuiteSparse_config -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -Wall -g -O2 -I/Users/rehlab/anaconda2/include/libxml2 -I/Users/rehlab/anaconda2/include -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.2.9000\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd_valid.c -o cigraph/src/AMD/Source/amd_valid.o
gfortran  -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amdbar.f -o cigraph/src/AMD/Source/amdbar.o
gfortran: warning: couldn’t understand kern.osversion ‘15.6.0
Warning: Nonconforming tab character in column 1 of line 422

Currently the computer I am using has many files on it and has no backups so I am waiting for the new backup drive to arrive before I update.

Connorr0 · 2019-09-30T18:42:55Z

I got rid of the old version of gfortran and now it appears that R cannot find any installation. I think that this means that I will have to configure a makevars file. Did you have to do this for the gfortran 6.1?

brgew · 2019-09-30T19:25:16Z

Hi @Connorr0,

I have not configured a special Makevars file in order to build leidenbase on the Mac.

This is confusing. I don't know the best way to investigate but I can offer some thoughts
and suggestions.

Perhaps there are incompatibilities between R and/or between the various compilers and/or their libraries. Can you tell me how you installed the C, C++, FORTRAN compilers, and how you installed R? It may help to look at the information in the R Makeconf file, which should be in the directory, or a subdirectory of, R_HOME/etc. You can use the R command R.home() to find the R_HOME path. I think that the most relevant lines start with

CC =
CFLAGS =
CPICFLAGS =
CPPFLAGS =
CXX =
CXXCPP =
CXXFLAGS =
CXXPICFLAGS =
CXX98 =
CXX98FLAGS =
CXX98PICFLAGS =
CXX98STD =
CXX11 =
CXX11FLAGS =
CXX11PICFLAGS =
CXX11STD =
CXX14 =
CXX14FLAGS =
CXX14PICFLAGS =
CXX14STD =
CXX17 =
CXX17FLAGS =
CXX17PICFLAGS =
CXX17STD =
CXX_VISIBILITY =
DYLIB_EXT =
DYLIB_LD =
DYLIB_LDFLAGS =
DYLIB_LINK =
FC =
FCFLAGS =
FCLIBS_XTRA =
FFLAGS =
FLIBS =

In your earlier message, you included warnings from gfortran but no errors. Yet it appears that the
linker cannot find the shared object file that it needs. Maybe there is no shared object file or it's not
where the linker is looking for it?

Connorr0 · 2019-09-30T20:37:09Z

R installation: Updated using updateR()
fortran complier: Downloaded from link and installed in default location. This appears to be in (/usr/local/gfortran/)

/usr/local/gfortran/lib contains:

i386			libgfortran.3.dylib	libquadmath.la
libasan.3.dylib		libgfortran.a		libsanitizer.spec
libasan.dylib		libgfortran.dylib	libssp.0.dylib
libasan.la		libgfortran.la		libssp.a
libasan_preinit.o	libgfortran.spec	libssp.dylib
libatomic.1.dylib	libgomp.1.dylib		libssp.la
libatomic.a		libgomp.a		libssp_nonshared.a
libatomic.dylib		libgomp.dylib		libssp_nonshared.la
libatomic.la		libgomp.la		libstdc++.6.dylib
libcc1.0.so		libgomp.spec		libstdc++.a
libcc1.la		libitm.1.dylib		libstdc++.a-gdb.py
libcc1.so		libitm.a		libstdc++.dylib
libcilkrts.5.dylib	libitm.dylib		libstdc++.la
libcilkrts.a		libitm.la		libstdc++fs.a
libcilkrts.dylib	libitm.spec		libstdc++fs.la
libcilkrts.la		libobjc-gnu.4.dylib	libsupc++.a
libcilkrts.spec		libobjc-gnu.a		libsupc++.la
libgcc_ext.10.4.dylib	libobjc-gnu.dylib	libubsan.0.dylib
libgcc_ext.10.5.dylib	libobjc-gnu.la		libubsan.dylib
libgcc_s.1.dylib	libquadmath.0.dylib	libubsan.la
libgcc_s_ppc64.1.dylib	libquadmath.a```

Makeconf (fortran section):
```## FC is the compiler used for all Fortran as from R 3.6.0
FC = gfortran
FCFLAGS = -Wall -g -O2 $(LTO)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS_XTRA = 
FFLAGS = -Wall -g -O2 $(LTO)
FLIBS =  -L/usr/local/gfortran/lib -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -lgfortran -lquadmath -lm

*I removed the fortran previously found in this location
Current output of devtools::install_github('cole-trapnell-lab/leidenbase'):

gfortran  -fPIC  -Wall -g -O2  -c cigraph/src/AMD/Source/amd.f -o cigraph/src/AMD/Source/amd.o
make: gfortran: No such file or directory
make: *** [cigraph/src/AMD/Source/amd.o] Error 1
ERROR: compilation failed for package ‘leidenbase’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:```

I tried changing the FC to /usr/local/gfortran, but I get a `Permission denied` error. Any advice? I could give more information if that would be helpful.

brgew · 2019-09-30T22:20:47Z

Hi @Connorr0,

I'm confused about some of the details I see. Let's start with R. How did you install R originally? Did
you download and installer from CRAN, build from source code manually, or use a package
manager, or something else? Next can you tell me the clang version that you are using and where
it is installed? You can get this information with the commands

type clang
clang --version

And you need gfortran installed, so if you have not reinstalled it at /usr/local/gfortran using the
package at https://cran.r-project.org/bin/macosx/tools/gfortran-6.1.pkg, you will need to do so.

Connorr0 · 2019-10-01T00:34:33Z

R was installed using the updateR() function from the package https://github.com/AndreaCirilloAC/updateR

I thought I installed clang but when I run type clang I get:
Error: unexpected symbol in "type clang"

/usr/local/gfortran appears to be populated.

brgew · 2019-10-01T16:56:54Z

Hi @Connorr0 ,

I may be unable to help you with these problems. I don't see how you installed R initially and the error message for 'type clang' is unfamiliar to me (perhaps you are not running a bash shell).

I can tell you that I tested leidenbase on a MacBook Pro running Mac OS X 10.11. I installed the R
3.6.1 and gfortran 6.1 packages from CRAN. The C/C++ compilers are Xcode clang version 8.0.0
with the command line tools installed. With these packages I built and installed leidenbase
successfully.

Yesterday, as a check, I installed clang7 from CRAN, set my PATH environment variable to include
the clang7 installation bin directory, and built and installed leidenbase successfully.

I have no insight into the sources of the problems that you see.

I wish you success!

ncalistri · 2019-10-04T23:40:09Z

Similar to some other users, I had trouble installing the leidenbase package on a machine running MacOS X 10.11, and got some vague error message instead.

I solved the issue by reinstalling gfortran via homebrew:
brew cask install gfortran

brgew · 2019-10-04T23:46:13Z

Hi @ncalistri,

That is great. Thank you for reporting your solution.

yangrc3 · 2019-11-02T13:09:29Z

I also have the same problem with leidenbase compilation in the process of monocle3 installation .My Mac Pro runs MacOS X 10.14 and R 3.6.1.
To solve this trouble, I reinstralled clang7 in terminal ,like tractatus did，velocyto-team/velocyto.R#2. Remember change clang4 to clang7.
And also brew gfortran.

Connorr0 · 2019-11-11T21:42:43Z

I ended up installing clang with xcode-select --install and got Fortran working by installing via homebrew.

Connorr0 closed this as completed Nov 11, 2019

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