Unable to install leidenbase

[bsmith030465]

Hi,

I am trying to install monocle3 on RStudio and have to install leidenbase. I executed the command 'devtools::install_github('cole-trapnell-lab/leidenbase')', but get an error:

.
*** 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 '/Users/bst/Library/R/4.0/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so':
dlopen(/Users/bst/Library/R/4.0/library/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so, 6): Symbol not found: ___addtf3
Referenced from: /usr/local/lib/libquadmath.0.dylib
Expected in: /usr/local/lib/libgcc_s_x86_64.1.dylib
in /usr/local/lib/libquadmath.0.dylib
Error: loading failed
Execution halted
ERROR: loading failed

• removing ‘/Users/bst/Library/R/4.0/library/leidenbase’

=========== Details on gcc, gfortran ====
| => gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin19.6.0

| => gfortran --version
GNU Fortran (Homebrew GCC 10.2.0_4) 10.2.0

======================
My RStudio 'Makeconf' file shows:

AR = ar
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas
C_VISIBILITY =
CC = clang -mmacosx-version-min=10.13
CFLAGS = -Wall -g -O2 $(LTO)
CPICFLAGS = -fPIC
CPPFLAGS = -I/usr/local/include
CXX = clang++ -mmacosx-version-min=10.13 -std=gnu++11

Not used by anything in R, in particular not for the .cc.d rule

but used via R CMD config by several packages

CXXCPP = $(CXX) -E
CXXFLAGS = -Wall -g -O2 $(LTO)
CXXPICFLAGS = -fPIC
CXX11 = clang++ -mmacosx-version-min=10.13
CXX11FLAGS = -Wall -g -O2 $(LTO)
CXX11PICFLAGS = -fPIC
CXX11STD = -std=gnu++11
CXX14 = clang++ -mmacosx-version-min=10.13
CXX14FLAGS = -Wall -g -O2 $(LTO)
CXX14PICFLAGS = -fPIC
CXX14STD = -std=gnu++14
CXX17 = clang++ -mmacosx-version-min=10.13
CXX17FLAGS = -Wall -g -O2 $(LTO)
CXX17PICFLAGS = -fPIC
CXX17STD = -std=gnu++17
CXX20 = clang++ -mmacosx-version-min=10.13
CXX20FLAGS = -Wall -g -O2 $(LTO)
CXX20PICFLAGS = -fPIC
CXX20STD = -std=gnu++2a
CXX_VISIBILITY =
DYLIB_EXT = .dylib
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress# $(CFLAGS) $(CPICFLAGS)

should be used by packges for dylibs, but at the time of writing was not

DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C = \c
ECHO_N =
ECHO_T =
F_VISIBILITY =

FC is the compiler used for all Fortran as from R 3.6.0

FC = gfortran -mmacosx-version-min=10.13
FCFLAGS = -Wall -g -O2 $(LTO_FC)

additional libs needed when linking with $(FC), e.g. on some Oracle compilers

FCLIBS_XTRA =
FFLAGS = -Wall -g -O2 $(LTO_FC)
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
FPICFLAGS = -fPIC
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS = -framework Foundation
JAR = /usr/bin/jar

==============

My R sessionInfo() is:

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] rstudioapi_0.13 magrittr_2.0.1 usethis_2.0.1 devtools_2.3.2 pkgload_1.1.0
[6] R6_2.5.0 rlang_0.4.10 fastmap_1.1.0 tools_4.0.3 pkgbuild_1.2.0
[11] sessioninfo_1.1.1 cli_2.3.0 withr_2.4.1 ellipsis_0.3.1 remotes_2.2.0
[16] assertthat_0.2.1 rprojroot_2.0.2 lifecycle_1.0.0 crayon_1.4.1 processx_3.4.5
[21] purrr_0.3.4 callr_3.5.1 fs_1.5.0 ps_1.5.0 curl_4.3
[26] testthat_3.0.2 memoise_2.0.0 glue_1.4.2 cachem_1.0.4 compiler_4.0.3
[31] desc_1.2.0 prettyunits_1.1.1bst

What do I need to do? Thanks for your help!

[brgew]

Hi,

There may be conflicts with installed compilers. The error message says that a symbol is not found related to libraries in /usr/local/lib:

/usr/local/lib/libquadmath.0.dylib
/usr/local/lib/libgcc_s_x86_64.1.dylib

Your gfortran compiler says it is build by Homebrew and gcc says it's Apple clang. The Homebrew packages are supposed to be installed in something like '/usr/local/Cellar' and I expect the Apple clang-related libraries to be installed in a system-like directory, for example, /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib. (In my experience, user-installed software is installed in /usr/local/*). When I check the gcc version on my Mac, I get

gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin20.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

which coincides with my expectation. I am guessing that someone installed another compiler in /usr/local and either clang or gfortran is trying to link those libraries instead of their libraries. You might check for gcc and/or gfortran in /usr/local/bin. These are likely to link libraries in /usr/local/lib. If this is the case, I cannot confidently suggest a solution because you may have other software that was compiled with the compilers in /usr/local.

[cadyyuheng]

Hello,

I also encountered some issues installing leidenbase. I wonder if it's because of some dependencies of the package. Here's the error I got:

** 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 '/home/yfy/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-leidenbase/00new/leidenbase/libs/leidenbase.so':
  libicui18n.so.68: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/yfy/R/x86_64-pc-linux-gnu-library/4.0/leidenbase’
* restoring previous ‘/home/yfy/R/x86_64-pc-linux-gnu-library/4.0/leidenbase’
Error: Failed to install 'leidenbase' from GitHub:
  (converted from warning) installation of package '/tmp/RtmpQedji7/file1e281b74212f/leidenbase_0.1.2.tar.gz' had non-zero exit status

[mingwhy]

Hello,
I ran into the same issue when installing leidenbase, my mac OS is Monterey Version 12.1 and my R version is R 4.1.3.

Below solution works for me
I reinstalled gfortran with gfortran-Intel-11.2-Monterey.dmg, then modified the Makevar file as follows:

(base) .R $cat Makevars

LOC = /usr/local/gfortran
CC=$(LOC)/bin/gcc -fopenmp
CXX=$(LOC)/bin/g++ -fopenmp
CXX11 = $(LOC)/bin/g++ -fopenmp

## check that the version of gfortran, in my case, it's 11.2.0
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin21/11.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

And then the installation went smooth.