Comments (6)
jdblischak
commented on September 27, 2024
@bainadeashish What is the value of of GIT_URL? I suspect the issue is that the URL is incorrect.
# setup
docker run -it --rm condaforge/mambaforge bash
mamba create -n issue-23 r-base=4.0.2 r-devtools
conda activate issue-23
# This works fine
Rscript -e 'devtools::install_git("https://github.com/Rdatatable/data.table.git")'
# An incorrect URL leads to an error
Rscript -e 'devtools::install_git("https//github.com/")'
## Error: Failed to install 'unknown package' from Git:
## Error in 'git2r_remote_ls': unsupported URL protocol
## Execution haltedEnvironment (conda list):
$ conda list
# packages in environment at /opt/conda/envs/issue-23:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_1 conda-forge
binutils_linux-64 2.36 hf3e587d_32 conda-forge
bwidget 1.9.14 ha770c72_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h7f98852_1 conda-forge
ca-certificates 2021.5.30 ha878542_0 conda-forge
cairo 1.16.0 h9f066cc_1006 conda-forge
certifi 2021.5.30 py39hf3d152e_0 conda-forge
curl 7.76.1 h979ede3_1 conda-forge
fontconfig 2.13.1 hba837de_1005 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc_impl_linux-64 7.5.0 habd7529_19 conda-forge
gcc_linux-64 7.5.0 h47867f9_32 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
gfortran_impl_linux-64 7.5.0 h56cb351_19 conda-forge
gfortran_linux-64 7.5.0 h78c8a43_32 conda-forge
glib 2.68.3 h9c3ff4c_0 conda-forge
glib-tools 2.68.3 h9c3ff4c_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.6 he838d99_2 conda-forge
gxx_impl_linux-64 7.5.0 hd0bb8aa_19 conda-forge
gxx_linux-64 7.5.0 h555fc39_32 conda-forge
harfbuzz 2.7.2 ha5b49bf_1 conda-forge
icu 67.1 he1b5a44_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_14 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_1 conda-forge
lerc 2.2.1 h9c3ff4c_0 conda-forge
libblas 3.9.0 8_openblas conda-forge
libcblas 3.9.0 8_openblas conda-forge
libcurl 7.76.1 hc4aaa36_1 conda-forge
libdeflate 1.7 h7f98852_5 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-devel_linux-64 7.5.0 hda03d7c_19 conda-forge
libgcc-ng 11.1.0 hc902ee8_0 conda-forge
libgfortran-ng 7.5.0 h14aa051_19 conda-forge
libgfortran4 7.5.0 h14aa051_19 conda-forge
libgit2 1.1.0 h0b03e73_0 conda-forge
libglib 2.68.3 h3e27bee_0 conda-forge
libgomp 11.1.0 hc902ee8_0 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 8_openblas conda-forge
libnghttp2 1.43.0 h812cca2_0 conda-forge
libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libssh2 1.9.0 ha56f1ee_6 conda-forge
libstdcxx-devel_linux-64 7.5.0 hb016644_19 conda-forge
libstdcxx-ng 11.1.0 h56837e0_0 conda-forge
libtiff 4.3.0 hf544144_1 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.0 h7f98852_2 conda-forge
libxcb 1.13 h7f98852_1003 conda-forge
libxml2 2.9.10 h68273f3_2 conda-forge
lz4-c 1.9.3 h9c3ff4c_0 conda-forge
make 4.3 hd18ef5c_1 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
openssl 1.1.1k h7f98852_0 conda-forge
pango 1.42.4 h69149e4_5 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.35 h032f7d1_2 conda-forge
pip 21.1.3 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
python 3.9.6 h49503c6_1_cpython conda-forge
python_abi 3.9 2_cp39 conda-forge
r-askpass 1.1 r40hcfec24a_2 conda-forge
r-assertthat 0.2.1 r40hc72bb7e_2 conda-forge
r-backports 1.2.1 r40hcfec24a_0 conda-forge
r-base 4.0.2 he766273_1 conda-forge
r-base64enc 0.1_3 r40hcfec24a_1004 conda-forge
r-brew 1.0_6 r40hc72bb7e_1003 conda-forge
r-brio 1.1.2 r40hcfec24a_0 conda-forge
r-cachem 1.0.5 r40hcfec24a_0 conda-forge
r-callr 3.7.0 r40hc72bb7e_0 conda-forge
r-cli 3.0.1 r40hc72bb7e_0 conda-forge
r-clipr 0.7.1 r40hc72bb7e_0 conda-forge
r-commonmark 1.7 r40hcfec24a_1002 conda-forge
r-covr 3.5.1 r40h03ef668_0 conda-forge
r-crayon 1.4.1 r40hc72bb7e_0 conda-forge
r-credentials 1.3.0 r40hc72bb7e_0 conda-forge
r-crosstalk 1.1.1 r40hc72bb7e_0 conda-forge
r-curl 4.3.2 r40hcfec24a_0 conda-forge
r-desc 1.3.0 r40hc72bb7e_0 conda-forge
r-devtools 2.4.2 r40hc72bb7e_0 conda-forge
r-diffobj 0.3.4 r40hcfec24a_0 conda-forge
r-digest 0.6.27 r40h03ef668_0 conda-forge
r-dt 0.18 r40hc72bb7e_0 conda-forge
r-ellipsis 0.3.2 r40hcfec24a_0 conda-forge
r-evaluate 0.14 r40hc72bb7e_2 conda-forge
r-fansi 0.5.0 r40hcfec24a_0 conda-forge
r-fastmap 1.1.0 r40h03ef668_0 conda-forge
r-fs 1.5.0 r40h03ef668_0 conda-forge
r-gert 1.3.1 r40hbd84cd2_0 conda-forge
r-gh 1.3.0 r40hc72bb7e_0 conda-forge
r-git2r 0.28.0 r40hf628c3e_0 conda-forge
r-gitcreds 0.1.1 r40hc72bb7e_0 conda-forge
r-glue 1.4.2 r40hcfec24a_0 conda-forge
r-highr 0.9 r40hc72bb7e_0 conda-forge
r-htmltools 0.5.1.1 r40h03ef668_0 conda-forge
r-htmlwidgets 1.5.3 r40hc72bb7e_0 conda-forge
r-httr 1.4.2 r40hc72bb7e_0 conda-forge
r-ini 0.3.1 r40hc72bb7e_1003 conda-forge
r-jsonlite 1.7.2 r40hcfec24a_0 conda-forge
r-knitr 1.33 r40hc72bb7e_0 conda-forge
r-later 1.2.0 r40h03ef668_0 conda-forge
r-lazyeval 0.2.2 r40hcfec24a_2 conda-forge
r-lifecycle 1.0.0 r40hc72bb7e_0 conda-forge
r-magrittr 2.0.1 r40hcfec24a_1 conda-forge
r-markdown 1.1 r40hcfec24a_1 conda-forge
r-memoise 2.0.0 r40hc72bb7e_0 conda-forge
r-mime 0.11 r40hcfec24a_0 conda-forge
r-openssl 1.4.4 r40he36bf35_0 conda-forge
r-pillar 1.6.1 r40hc72bb7e_0 conda-forge
r-pkgbuild 1.2.0 r40hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r40hc72bb7e_1 conda-forge
r-pkgload 1.2.1 r40h03ef668_0 conda-forge
r-praise 1.0.0 r40hc72bb7e_1004 conda-forge
r-prettyunits 1.1.1 r40hc72bb7e_1 conda-forge
r-processx 3.5.2 r40hcfec24a_0 conda-forge
r-promises 1.2.0.1 r40h03ef668_0 conda-forge
r-ps 1.6.0 r40hcfec24a_0 conda-forge
r-purrr 0.3.4 r40hcfec24a_1 conda-forge
r-r6 2.5.0 r40hc72bb7e_0 conda-forge
r-rappdirs 0.3.3 r40hcfec24a_0 conda-forge
r-rcmdcheck 1.3.3 r40hc72bb7e_3 conda-forge
r-rcpp 1.0.7 r40h03ef668_0 conda-forge
r-rematch2 2.1.2 r40hc72bb7e_1 conda-forge
r-remotes 2.4.0 r40hc72bb7e_0 conda-forge
r-rex 1.2.0 r40hc72bb7e_1 conda-forge
r-rlang 0.4.11 r40hcfec24a_0 conda-forge
r-roxygen2 7.1.1 r40h03ef668_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-rversions 2.1.1 r40hc72bb7e_0 conda-forge
r-sessioninfo 1.1.1 r40hc72bb7e_1002 conda-forge
r-stringi 1.5.3 r40hca8494e_0 conda-forge
r-stringr 1.4.0 r40hc72bb7e_2 conda-forge
r-sys 3.4 r40hcfec24a_0 conda-forge
r-testthat 3.0.4 r40h03ef668_0 conda-forge
r-tibble 3.1.3 r40hcfec24a_0 conda-forge
r-usethis 2.0.1 r40hc72bb7e_0 conda-forge
r-utf8 1.2.1 r40hcfec24a_0 conda-forge
r-vctrs 0.3.8 r40hcfec24a_1 conda-forge
r-waldo 0.2.5 r40hc72bb7e_0 conda-forge
r-whisker 0.4 r40hc72bb7e_1 conda-forge
r-withr 2.4.2 r40hc72bb7e_0 conda-forge
r-xfun 0.24 r40h03ef668_0 conda-forge
r-xml2 1.3.2 r40h03ef668_1 conda-forge
r-xopen 1.0.0 r40hc72bb7e_1003 conda-forge
r-yaml 2.2.1 r40hcfec24a_1 conda-forge
r-zip 2.2.0 r40hcfec24a_0 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
setuptools 49.6.0 py39hf3d152e_3 conda-forge
sqlite 3.36.0 h9cd32fc_0 conda-forge
sysroot_linux-64 2.12 he073ed8_14 conda-forge
tk 8.6.10 h21135ba_1 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
tzdata 2021a he74cb21_1 conda-forge
wheel 0.36.2 pyhd3deb0d_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.5.0 ha95c52a_0 conda-forge
Details about
conda and system ( conda info ):
$ conda info
active environment : issue-23
active env location : /opt/conda/envs/issue-23
shell level : 2
user config file : /root/.condarc
populated config files : /opt/conda/.condarc
conda version : 4.10.3
conda-build version : not installed
python version : 3.9.6.final.0
virtual packages : __linux=5.10.25=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /opt/conda (writable)
conda av data dir : /opt/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /opt/conda/pkgs
/root/.conda/pkgs
envs directories : /opt/conda/envs
/root/.conda/envs
platform : linux-64
user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.6 Linux/5.10.25-linuxkit ubuntu/20.04.2 glibc/2.31
UID:GID : 0:0
netrc file : None
offline mode : False
from r-devtools-feedstock.
bainadeashish
commented on September 27, 2024
no value of GIT_URL is correct, same is working fine with cran devtools but fails in r-devtools conda.
@jdblischak
from r-devtools-feedstock.
jdblischak
commented on September 27, 2024
no value of GIT_URL is correct, same is working fine with cran devtools but fails in r-devtools conda.
We need a minimal reproducible example to be able to troubleshoot the issue you are having. Could you please run the code below and report back whether or not it successfully runs for you?
conda create --yes -n test-install-git --override-channels -c conda-forge r-base=4.0.2 r-devtools
conda activate test-install-git
Rscript -e 'devtools::install_git("https://github.com/HenrikBengtsson/R.utils")'
conda deactivatefrom r-devtools-feedstock.
bainadeashish
commented on September 27, 2024
@jdblischak let me try & will update accordingly.
Thanks alot
from r-devtools-feedstock.
bainadeashish
commented on September 27, 2024
Its working fine for URL you mentioned but somehow its failing for below URL
Step 24/40 : RUN Rscript -e 'devtools::install_git("https://gitlab+deploy-token-49:MVJMoJQbGThZbdzEb@GIT_REPO.git")'
---> Running in 8b5f6302861e
WARNING: ignoring environment value of R_HOME
Error: Failed to install 'unknown package' from Git:
Error in 'git2r_remote_ls': malformed URL 'https://gitlab+deploy-token-49:MVJMoJQbGThZbdzEb'
Replaced actual repo name with GIT_REPO due to security issues.
from r-devtools-feedstock.
jdblischak
commented on September 27, 2024
Its working fine for URL you mentioned but somehow its failing for below URL
OK, great. Thanks for confirming. This is a good sign. It will work for the most standard use case of installing from a public repo.
Error in 'git2r_remote_ls': malformed URL 'https://gitlab+deploy-token-49:MVJMoJQbGThZbdzEb'
I don't have any experience with authenticating with a GitLab deploy token. This URL works with devtools installed from CRAN? If yes, my only guess is that there is some difference in the authentication features when installing libgit2. Can you try running git2r::libgit2_features() with both your CRAN setup and in your conda environment? Are there are any differences in the enabled features?
Some other ideas to consider:
-
What happens if you try setting
git = "external"? This should use your system Git instead of git2r (which is where the error is coming from). If you don't have Git installed, you can runconda install git. -
If you need to use private repos on GitLab, I'd recommend generating a GitLab PAT, saving it in the environment variable
GITHUB_PAT, and then installing withinstall_gitlab() -
There's nothing particularly special about
install_git(). If you're having trouble getting it to authenticate with your URL, you can clone it and then install itgit clone https://gitlab+deploy-token-49:MVJMoJQbGThZbdzEb@GIT_REPO.git Rscript -e 'devtools::install("GIT_REPO")'
from r-devtools-feedstock.
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