[Bioc-devel] Question reg devtools in MacOS High Sierra

[Krithika Bhuvaneshwar]

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BiocManager::valid()              # checks for out of date packages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.bioc using 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-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 ?
>
>     Thanks,
>     Krithika
>
>
>
>     On Thu, Feb 11, 2021 at 12:03 PM Nitesh Turaga <nturaga.bioc using 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-bounces using r-project.org on behalf of kb472 using 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
>     >
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>     >
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>     >
>

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