[Bioc-devel] Question reg devtools in MacOS High Sierra
kb472 @end|ng |rom georgetown@edu
Fri Feb 12 04:06:53 CET 2021
Thank you very much Martin, that was very helpful ! I had failed to catch
When I ran "brew install openssl", it was already present in my mac, but I
had to run install.packages("openssl") again for it to work.
In case this is helpful to anyone, here is a full list of things I did to
get the development environment up and running on Mac High Sierra:
# downloaded R 4.1 from https://mac.r-project.org/
# Got the latest BioC 3.13 using BiocManager::install(version = "devel")
if (!requireNamespace("BiocManager", quietly=TRUE))
BiocManager::install(version = "devel")
BiocManager::valid() # checks for out of date packages
#Install dependencies for devtools
brew install libgit2
brew install openssl # if needed
#install package related dependencies - for your package
On Thu, Feb 11, 2021 at 6:45 PM Martin Morgan <mtmorgan.bioc using gmail.com>
> The error says
> unable to load shared object
> so it's having trouble loading the openssl R package. There are
> installation instructions for this package at
> (I found this from the CRAN package landing page
> https://cran.r-project.org/package=openssl 'URL' field) There it says
> that to install on macOS you need to
> brew install openssl
> In general the strategy is to start at the first ERROR that occurs, and
> carefully try to 'decode' what it is trying to tell you.
> The problem you are running into is that the 'release' version of macOS
> CRAN packages are generally available as pre-built 'binary' packages, so
> you don't have to do anything special to make them work. The 'devel'
> version of macOS CRAN packages are not available for binary installation,
> so you have to have additional system dependencies like libgit2 and openssl
> also installed.
> On 2/11/21, 6:06 PM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" <
> bioc-devel-bounces using r-project.org on behalf of kb472 using georgetown.edu> wrote:
> Hi Nitesh,
> Thanks for your reply.
> I managed to get libgit2 installed. But having trouble with its other
> dependencies - ‘gert’
> Please see attached txt which is a full information of the error.
> Do you have an installation of R 4.1 that is more stable where
> devtools is
> working ? If yes, are you able to share that with me ?
> On Thu, Feb 11, 2021 at 12:03 PM Nitesh Turaga <nturaga.bioc using gmail.com
> > Hi,
> > Could you provide more information about the error you face with
> > install libgit2` ?? Without knowing what error message you see, it's
> > to speculate about why devtools or gert didn’t work.
> > Best,
> > On 2/11/21, 12:00 AM, "Bioc-devel on behalf of Krithika
> Bhuvaneshwar" <
> > bioc-devel-bounces using r-project.org on behalf of kb472 using georgetown.edu>
> > Hello,
> > We are the package maintainers of the CINdex package. Our
> package is
> > giving
> > build errors and we are investigating why. I'm currently working
> > setting
> > up the environment so I can replicate the error.
> > I have a MacOS High Sierra. Here is what I did:
> > * downloaded R 4.1 from https://mac.r-project.org/ and
> > * Got the latest BioC 3.13 using BiocManager::install(version =
> > "devel")
> > * When I tried *install.packages("devtools")*, it said
> > *"Package which is only available in source form, and may need
> > compilation
> > of **C/C++/Fortran: ‘gert’*
> > So Then I did *install.packages("devtools")*
> > It gave me an error saying
> > *"Configuration failed to find libgit2 library." Try installing:
> > libgit2 (MacOS)*
> > I have tried installing libgit2 using both brew and within R.
> > worked. So at this point, I'm unable to install devtools . And
> > devtools, Check And Build are not working
> > Has anyone else encountered this issue, please advise on how to
> > this.
> > Thanks,
> > Krithika
> > [[alternative HTML version deleted]]
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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