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
>
> install.packages("devtools")
also installing the dependencies âgertâ, âusethisâ
Warning in install.packages :
unable to access index for repository
https://cran.rstudio.com/bin/macosx/contrib/4.1:
cannot open URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/PACKAGES'
Package which is only available in source form, and may need compilation of
C/C++/Fortran: âgertâ
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source packages âgertâ, âusethisâ, âdevtoolsâ
trying URL 'https://cran.rstudio.com/src/contrib/gert_1.1.0.tar.gz'
Content type 'application/x-gzip' length 67224 bytes (65 KB)
==================================================
downloaded 65 KB
trying URL 'https://cran.rstudio.com/src/contrib/usethis_2.0.1.tar.gz'
Content type 'application/x-gzip' length 306090 bytes (298 KB)
==================================================
downloaded 298 KB
trying URL 'https://cran.rstudio.com/src/contrib/devtools_2.3.2.tar.gz'
Content type 'application/x-gzip' length 373387 bytes (364 KB)
==================================================
downloaded 364 KB
* installing *source* package âgertâ ...
** package âgertâ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/local/Cellar/libgit2/1.1.0/include
Using PKG_LIBS=-L/usr/local/Cellar/libgit2/1.1.0/lib -lgit2
Configuration OK!
** libs
rm -f gert.so branch.o clone.o commit.o config.o conflicts.o files.o init.o
merge.o rebase.o stash.o submodules.o tag.o utils.o version.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c branch.c -o branch.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c clone.c -o clone.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c commit.c -o commit.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c config.c -o config.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c conflicts.c -o conflicts.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c files.c -o files.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c merge.c -o merge.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c rebase.c -o rebase.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c stash.c -o stash.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c submodules.c -o submodules.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c tag.c -o tag.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/Cellar/libgit2/1.1.0/include -DR_NO_REMAP -DSTRICT_R_HEADERS
-I/usr/local/include -fPIC -Wall -g -O2 -c version.c -o version.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o gert.so
branch.o clone.o commit.o config.o conflicts.o files.o init.o merge.o rebase.o
stash.o submodules.o tag.o utils.o version.o
-L/usr/local/Cellar/libgit2/1.1.0/lib -lgit2
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
ld: warning: text-based stub file
/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and
library file
/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of
sync. Falling back to library file for linking.
installing to
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-gert/00new/gert/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl/libs/openssl.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl/libs/openssl.so,
6): Library not loaded: /usr/local/opt/openssl/lib/libssl.1.0.0.dylib
Referenced from:
/Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl/libs/openssl.so
Reason: image not found
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package âgertâ
* removing
â/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gertâ
Warning in install.packages :
installation of package âgertâ had non-zero exit status
ERROR: dependency âgertâ is not available for package âusethisâ
* removing
â/Library/Frameworks/R.framework/Versions/4.1/Resources/library/usethisâ
Warning in install.packages :
installation of package âusethisâ had non-zero exit status
ERROR: dependency âusethisâ is not available for package âdevtoolsâ
* removing
â/Library/Frameworks/R.framework/Versions/4.1/Resources/library/devtoolsâ
Warning in install.packages :
installation of package âdevtoolsâ had non-zero exit status
The downloaded source packages are in
â/private/var/folders/hd/yz81jsl14dx__mdn2gmctk6c0000gp/T/RtmpQW5saW/downloaded_packagesâ
Warning message:
R graphics engine version 14 is not supported by this version of RStudio. The
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