Thank you very much Martin, that was very helpful ! I had failed to catch
that.
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))
install.packages("BiocManager")
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BiocManager::valid() # checks for out of date packages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.packages("openssl")
install.packages("gert")
install.packages("usethis")
install.packages("devtools")
library(devtools)
#install package related dependencies - for your package
Thanks,
Krithika
On Thu, Feb 11, 2021 at 6:45 PM Martin Morgan <mtmorgan.b...@gmail.com>
wrote:
> The error says
>
> unable to load shared object
> '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl/libs/openssl.so':
>
> so it's having trouble loading the openssl R package. There are
> installation instructions for this package at
>
> https://github.com/jeroen/openssl#readme
>
> (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.
>
> Martin
>
>
> On 2/11/21, 6:06 PM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" <
> bioc-devel-boun...@r-project.org on behalf of kb...@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 ?
>
> Thanks,
> Krithika
>
>
>
> On Thu, Feb 11, 2021 at 12:03 PM Nitesh Turaga <nturaga.b...@gmail.com
> >
> wrote:
>
> > Hi,
> >
> > Could you provide more information about the error you face with
> `brew
> > install libgit2` ?? Without knowing what error message you see, it's
> hard
> > 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-boun...@r-project.org on behalf of kb...@georgetown.edu>
> wrote:
> >
> > 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
> on
> > 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:
> brew:
> > libgit2 (MacOS)*
> > I have tried installing libgit2 using both brew and within R.
> Neither
> > worked. So at this point, I'm unable to install devtools . And
> without
> > devtools, Check And Build are not working
> >
> > Has anyone else encountered this issue, please advise on how to
> fix
> > this.
> >
> > Thanks,
> > Krithika
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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