Issue installing Monocle3 (Rcpp)

[cgraham13]

Hello,

I had Monocle3 working beautifully last week but I just updated my R version on my Mac to 4.2.1 and now I can no longer get it to install. I have downloaded the latest version of gfortran as well.

Here is the error I am getting:

devtools::install_github('cole-trapnell-lab/monocle3') Downloading GitHub repo cole-trapnell-lab/monocle3@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: cli (3.3.0 -> 3.4.0) [CRAN] 5: httpuv (1.6.5 -> 1.6.6) [CRAN] 6: tidyr (1.2.0 -> 1.2.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 1 cli (3.3.0 -> 3.4.0) [CRAN] httpuv (1.6.5 -> 1.6.6) [CRAN] tidyr (1.2.0 -> 1.2.1) [CRAN] Installing 3 packages: cli, httpuv, tidyr

There are binary versions available but the source versions are later: binary source needs_compilation cli 3.3.0 3.4.0 TRUE httpuv 1.6.5 1.6.6 TRUE tidyr 1.2.0 1.2.1 TRUE

Do you want to install from sources the packages which need compilation? (Yes/no/cancel) no trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/cli_3.3.0.tgz' Content type 'application/x-gzip' length 1160100 bytes (1.1 MB)

downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/httpuv_1.6.5.tgz' Content type 'application/x-gzip' length 2746898 bytes (2.6 MB)

downloaded 2.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/tidyr_1.2.0.tgz' Content type 'application/x-gzip' length 1001459 bytes (977 KB)

downloaded 977 KB

The downloaded binary packages are in /var/folders/jk/4pbws9cx0_15lwmtmjv6dn0m0000gn/T//RtmpuwzIgB/downloaded_packages ✔ checking for file ‘/private/var/folders/jk/4pbws9cx0_15lwmtmjv6dn0m0000gn/T/RtmpuwzIgB/remotes15202e5c7bac/cole-trapnell-lab-monocle3-87f6e88/DESCRIPTION’ ... ─ preparing ‘monocle3’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories Omitted ‘LazyData’ from DESCRIPTION ─ building ‘monocle3_1.2.9.tar.gz’

• installing source package ‘monocle3’ ... using staged installation libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100: In file included from /usr/local/include/c++/v1/cmath:305: /usr/local/include/c++/v1/math.h:301:15: fatal error: 'math.h' file not found

  include_next

        ^~~~~~~~

  1 error generated. make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘monocle3’

• removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/monocle3’ Warning message: In i.p(...) : installation of package ‘/var/folders/jk/4pbws9cx0_15lwmtmjv6dn0m0000gn/T//RtmpuwzIgB/file15204870d8d3/monocle3_1.2.9.tar.gz’ had non-zero exit status

Any help would be great!

Carly

[Dongjie-orange]

i met the same problem,the same as the Mac OS M1 Pro chip

[Streisenberg]

I also encountered the same error.

macOS Monterey:12.6.5 Apple M1 Max chip R.version: 4.3.1