I´m trying to install the package NormqPCR and I have to update two packages, igraph and spdep, but until now I couldn´t and I can´t figure out what I must supouse to do. This is the code.
if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install("NormqPCR", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'NormqPCR'
trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/macosx/el-capitan/contrib/3.5/NormqPCR_1.28.0.tgz'
Content type 'application/x-gzip' length 425843 bytes (415 KB)
==================================================
downloaded 415 KB
The downloaded binary packages are in
/var/folders/1d/n28vx45163z4ksd8pcqxjwzh0000gn/T//Rtmpb5GHtX/downloaded_packages
Update old packages: 'BiocInstaller', 'igraph', 'spdep'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
igraph 1.2.3 1.2.4 TRUE
spdep 0.8-1 1.0-2 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) Yes
trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/macosx/el-capitan/contrib/3.5/BiocInstaller_1.32.1.tgz'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
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: *** [spdep.so] Error 1
ERROR: compilation failed for package ‘spdep’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/spdep’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/spdep’
The downloaded source packages are in
‘/private/var/folders/1d/n28vx45163z4ksd8pcqxjwzh0000gn/T/Rtmpb5GHtX/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘igraph’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘spdep’ had non-zero exit status
>
Anyone know a posible solution? Thanks!!
I just ran into this today as well after updating to R 3.5.
Looks like a solution is here.
Basically, its install gfortran 6.3.0, and set environment variables in the an ~/.R/Makevars file.
I haven't really used it yet, but it loads without error now. This is 'just' a dependency for me, and I'm not even 100% sure anything I'll do will use