mgcv not updating
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Aliza ▴ 10
@aliza-24804
Last seen 9 weeks ago

Hi I am new to Bioconductor and I am trying to install easyRNASeq and DESeq2 but neither will install because the version of mgcv available is 1.8-33. It needs to be updated to 1.8-34. I tried to do this but keep getting the error below. Any advice on how to get this debugged?

> install.packages("mgcv")

  There is a binary version available but the source version is later:
     binary source needs_compilation
mgcv 1.8-33 1.8-34              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘mgcv’

trying URL 'https://cran.rstudio.com/src/contrib/mgcv_1.8-34.tar.gz'
Content type 'application/x-gzip' length 1149538 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c coxph.c -o coxph.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c davies.c -o davies.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c discrete.c -o discrete.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gdi.c -o gdi.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c magic.c -o magic.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mat.c -o mat.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix.c -o matrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mgcv.c -o mgcv.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c misc.c -o misc.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c mvn.c -o mvn.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c qp.c -o qp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c soap.c -o soap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sparse-smooth.c -o sparse-smooth.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sparse.c -o sparse.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tprs.c -o tprs.o

clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mgcv.so] Error 1
ERROR: compilation failed for package ‘mgcv’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/mgcv’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/mgcv’
Warning in install.packages :
  installation of package ‘mgcv’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/xb/x046hrrd33xgqr1nlkrp5zs00000gq/T/RtmpCtCY2M/downloaded_packages’
mgcv easyRNASeq • 109 views
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You probably want to install the latest gfortran and clang versions to compile packages from source on a Mac, see https://cran.r-project.org/bin/macosx/tools/

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Do you really need to use version 1.8-33? 1.8.34 was published in source from yesterday (on the 16th of February, https://cran.r-project.org/web/packages/mgcv/index.html) and the Windows and macOS binaries will be updated in the next day or so. It will be much easier to wait for these to become available than to install the package from source yourself.

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