Trying to install ensembldb in Rstudio 3.6.3

[noodlebasket1]

Hello, I'm trying to install ensembldb in Rstudio 3.6.3 on my Macbook Air (MacOS Montery) and receive the following error:

BiocManager::install("ensembldb") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.10 (BiocManager 1.30.23), R 3.6.3 (2020-02-29) Old packages: 'cluster', 'KernSmooth', 'mgcv', 'nlme' Update all/some/none? [a/s/n]: a Warning: unable to access index for repository https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6: cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES' Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘cluster’ ‘KernSmooth’ ‘mgcv’ ‘nlme’ Do you want to attempt to install these from sources? (Yes/no/cancel) Yes installing the source packages ‘cluster’, ‘KernSmooth’, ‘mgcv’, ‘nlme’

trying URL 'https://cran.rstudio.com/src/contrib/cluster_2.1.6.tar.gz' Content type 'application/x-gzip' length 369050 bytes (360 KB)

downloaded 360 KB

trying URL 'https://cran.rstudio.com/src/contrib/KernSmooth_2.23-22.tar.gz' Content type 'application/x-gzip' length 25996 bytes (25 KB)

downloaded 25 KB

trying URL 'https://cran.rstudio.com/src/contrib/mgcv_1.9-1.tar.gz' Content type 'application/x-gzip' length 1083217 bytes (1.0 MB)

downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-164.tar.gz' Content type 'application/x-gzip' length 836832 bytes (817 KB)

downloaded 817 KB

• installing source package ‘cluster’ ... package ‘cluster’ successfully unpacked and MD5 sums checked using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c clara.c -o clara.o gfortran -fPIC -Wall -g -O2 -c daisy.f -o daisy.o make: gfortran: No such file or directory make: *** [daisy.o] Error 1 ERROR: compilation failed for package ‘cluster’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cluster’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cluster’
• installing source package ‘KernSmooth’ ... package ‘KernSmooth’ successfully unpacked and MD5 sums checked using staged installation ** libs gfortran -fPIC -Wall -g -O2 -c blkest.f -o blkest.o make: gfortran: No such file or directory make: *** [blkest.o] Error 1 ERROR: compilation failed for package ‘KernSmooth’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/KernSmooth’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/KernSmooth’
• installing source package ‘nlme’ ... package ‘nlme’ successfully unpacked and MD5 sums checked using staged installation ** libs gfortran -fPIC -Wall -g -O2 -c chol.f -o chol.o make: gfortran: No such file or directory make: *** [chol.o] Error 1 ERROR: compilation failed for package ‘nlme’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nlme’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nlme’
• 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 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c coxph.c -o coxph.o clang: error: unsupported option '-fopenmp' make: *** [coxph.o] Error 1 ERROR: compilation failed for package ‘mgcv’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mgcv’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/mgcv’

The downloaded source packages are in ‘/private/var/folders/fm/sjxn7fbd4zj1xbt31ldp78z00000gn/T/Rtmp26HJTi/downloaded_packages’ Warning messages: 1: package(s) not installed when version(s) same as or greater than current; use force = TRUE to re-install: 'ensembldb' 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘cluster’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘KernSmooth’ had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘nlme’ had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘mgcv’ had non-zero exit status

Every time I try to install the dependencies one by one, the same error pops up that the other dependencies are needed. Any suggestions?

[noodlebasket1]

As for the "fopenmp" issue for the mgcv dependency, I tried using: Sys.setenv(USE_OPENMP = "no") install.packages("mgcv", type = "source")

but to no avail

[jorainer]

Note ensembldb does not depend on or require/import the mgcv package. you could simply say n to the question Update all/some/none.

Also (but unrelated), you are using a pretty old version of R/Bioconductor - maybe you could consider updating to R 4.0.0 / Bioconductor 3.19 too?