monocle3 installation issues - r

Question

I have R 4.2.1 and the latest R studio build 554 on a macOS Monterey.
I am trying to install monocle3 using the following :
BiocManager::install('monocle3')
I get a really long error message
BiocManager::install("monocle3")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Installing package(s) 'monocle3'
Old packages: 'processx', 'ps', 'tm', 'zip'
Update all/some/none? [a/s/n]:
a
There are binary versions available but the source versions are later:
binary source needs_compilation
processx 3.7.0 3.8.0 TRUE
ps 1.7.1 1.7.2 TRUE
tm 0.7-8 0.7-9 TRUE
zip 2.2.1 2.2.2 TRUE
Do you want to install from sources the packages which need compilation? (Yes/no/cancel) yes
installing the source packages ‘processx’, ‘ps’, ‘tm’, ‘zip’
trying URL 'https://cran.rstudio.com/src/contrib/processx_3.8.0.tar.gz'
Content type 'application/x-gzip' length 162539 bytes (158 KB)
==================================================
downloaded 158 KB
trying URL 'https://cran.rstudio.com/src/contrib/ps_1.7.2.tar.gz'
Content type 'application/x-gzip' length 129096 bytes (126 KB)
==================================================
downloaded 126 KB
trying URL 'https://cran.rstudio.com/src/contrib/tm_0.7-9.tar.gz'
Content type 'application/x-gzip' length 638649 bytes (623 KB)
==================================================
downloaded 623 KB
trying URL 'https://cran.rstudio.com/src/contrib/zip_2.2.2.tar.gz'
Content type 'application/x-gzip' length 103404 bytes (100 KB)
==================================================
downloaded 100 KB
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -Wall -g -O2 -L/usr/local/lib -Wall px.c -o px
px.c:6:10: fatal error: 'unistd.h' file not found
#include <unistd.h>
^~~~~~~~~~
1 error generated.
make: *** [Makevars:11: px] Error 1
ERROR: compilation failed for package ‘ps’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ps’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ps’
* installing *source* package ‘tm’ ...
** package ‘tm’ successfully unpacked and MD5 sums checked
** 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/BH/include' -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 /Users/osman/opt/miniconda3/bin/../include/c++/v1/cmath:305:
/Users/osman/opt/miniconda3/bin/../include/c++/v1/math.h:301:15: fatal error: 'math.h' file not found
#include_next <math.h>
^~~~~~~~
1 error generated.
make: *** [/Library/Frameworks/R.framework/Resources/etc/Makeconf:175: RcppExports.o] Error 1
ERROR: compilation failed for package ‘tm’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/tm’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/tm’
* installing *source* package ‘zip’ ...
** package ‘zip’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -Wall -g -O2 miniz.c zip.c unixutils.c tools/cmdzip.c -o tools/cmdzip
In file included from miniz.c:27:
./miniz.h:156:10: fatal error: 'time.h' file not found
#include <time.h>
^~~~~~~~
1 error generated.
make: *** [Makevars:9: tools/cmdzip] Error 1
ERROR: compilation failed for package ‘zip’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zip’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zip’
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -Wall -g -O2 -L/usr/local/lib -Wall tools/px.c -o tools/px
tools/px.c:11:10: fatal error: 'unistd.h' file not found
#include <unistd.h>
^~~~~~~~~~
1 error generated.
make: *** [Makevars:14: tools/px] Error 1
ERROR: compilation failed for package ‘processx’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/processx’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/processx’
The downloaded source packages are in
‘/private/var/folders/ps/3jjkc4kj1y98mzlpdm3wp5dm0000gn/T/RtmpNbTlti/downloaded_packages’
Warning messages:
1: package ‘monocle3’ is not available for Bioconductor version '3.15'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
2: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘ps’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘tm’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘zip’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘processx’ had non-zero exit status
so I tried installing 'processx', 'ps', 'tm', 'zip' individually and now I get the following message:
Warning message:
package ‘monocle3’ is not available for Bioconductor version '3.15'
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Any idea for how to fix this issue?
I expected the installation to go through but it did not

Answer 1

When I get errors installing a package what I usually do is going to the first package that didn't install properly and try and install it in a different way, and I do the same for the others.
Other mac users had similar issue installing the ps package as you can see in this github issues here https://github.com/r-lib/ps/issues/55
they solved the problem by installing ps package via anaconda:
https://anaconda.org/conda-forge/r-ps