Cannot install NORMT3

[ruhollah2]

It appeared that NORMT3 has several dependencies, like gfortran and c-compiler . Even after installing these dependencies, NORMT3 cannot be installed with the following errer:

$ R CMD install NORMT3_1.0.4.tar.gz
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘NORMT3’ ...
** package ‘NORMT3’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c IPerfcvec.c -o IPerfcvec.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c IPwofzvec.c -o IPwofzvec.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c NORMT3_init.c -o NORMT3_init.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c toms680-1.f -o toms680-1.o
toms680-1.f:164:72:

  164 |             QLAMBDA = QLAMBDA/H2
      |                                                                        ^
Warning: ‘h2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
toms680-1.f:164:72: Warning: ‘qlambda’ may be used uninitialized in this function [-Wmaybe-uninitialized]
clang -mmacosx-version-min=10.13 -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 NORMT3.so IPerfcvec.o IPwofzvec.o NORMT3_init.o toms680-1.o -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-14: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [NORMT3.so] Error 1
ERROR: compilation failed for package ‘NORMT3’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/NORMT3’

Any help is highly appreciated?

MacOS Monterey
R version 4.1.1 (2021-08-10) -- "Kick Things"

[xiasijian]

[chrisamiller]

It appears that NORMT3 was removed from CRAM, but I was able to install it on MacOSX by grabbing the latest package from the archives: https://cran.r-project.org/src/contrib/Archive/NORMT3/

$ wget https://cran.r-project.org/src/contrib/Archive/NORMT3/NORMT3_1.0.4.tar.gz
$ R CMD install NORMT3_1.0.4.tar.gz
$ R --silent
> library(NORMT3)
NORMT3: Evaluates erf, erfc, Faddeeva functions and Gaussian/T sum densities
Copyright: Guy Nason 2005-2022
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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

other attached packages:
[1] NORMT3_1.0.4

loaded via a namespace (and not attached):
[1] compiler_4.2.0

Does this solution work for you?

[LorenzoBioinfo]

I tried downloading NORMT3 from https://cran.r-project.org/src/contrib/Archive/NORMT3/ but I got the same error of ruhollah2.

[chrisamiller]

I am seeing the same issue now on R version 4.3 and MacOSX 12.6. It's a fairly deep rabbit hole involving clang/gfortran versions that I don't have time to go down at the moment (but will check back on in the future).

In the meantime, I know that this docker image contains a working version of sciclone. You could give it a try until we're able to find a workaround:
https://hub.docker.com/r/seqfu/sciclone