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conda-forge / r-devtools-feedstock

A conda-smithy repository for r-devtools.
BSD 3-Clause "New" or "Revised" License
3 stars 6 forks source link

devtools::install_git fails #23

Open bainadeashish opened 3 years ago

bainadeashish commented 3 years ago

Issue: devtools::install_git fails for below cmd

devtools::install_git(GIT_URL) Error: Failed to install 'unknown package' from Git: Error in 'git2r_remote_ls': malformed URL 'GIT_URL'


Environment (conda list):

``` root@3f49d12504a3:/# conda list # packages in environment at /opt/miniconda: # # Name Version Build Channel _libgcc_mutex 0.1 main _r-mutex 1.0.1 anacondar_1 conda-forge binutils_impl_linux-64 2.33.1 he1b5a44_7 conda-forge binutils_linux-64 2.33.1 h9595d00_17 conda-forge brotlipy 0.7.0 py38h27cfd23_1003 bwidget 1.9.14 ha770c72_0 conda-forge bzip2 1.0.8 h516909a_3 conda-forge ca-certificates 2021.5.30 ha878542_0 conda-forge cairo 1.16.0 h3fc0475_1005 conda-forge certifi 2021.5.30 py38h578d9bd_0 conda-forge cffi 1.14.3 py38h261ae71_2 chardet 3.0.4 py38h06a4308_1003 conda 4.10.3 py38h578d9bd_0 conda-forge conda-package-handling 1.7.2 py38h03888b9_0 cryptography 3.2.1 py38h3c74f83_1 curl 7.71.1 he644dc0_3 conda-forge fontconfig 2.13.1 h7e3eb15_1002 conda-forge freetype 2.10.4 h7ca028e_0 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge gcc_impl_linux-64 7.3.0 habb00fd_1 gcc_linux-64 7.3.0 h553295d_17 conda-forge gfortran_impl_linux-64 7.3.0 hdf63c60_5 conda-forge gfortran_linux-64 7.3.0 h553295d_17 conda-forge glib 2.68.2 h36276a3_0 graphite2 1.3.13 h58526e2_1001 conda-forge gsl 2.6 hf94e986_0 conda-forge gxx_impl_linux-64 7.3.0 hdf63c60_1 gxx_linux-64 7.3.0 h553295d_17 conda-forge harfbuzz 2.7.2 hee91db6_0 conda-forge icu 67.1 he1b5a44_0 conda-forge idna 2.10 py_0 jpeg 9d h36c2ea0_0 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge ld_impl_linux-64 2.33.1 h53a641e_7 libblas 3.9.0 8_openblas conda-forge libcblas 3.9.0 8_openblas conda-forge libcurl 7.71.1 hcdd3856_3 conda-forge libedit 3.1.20191231 h14c3975_1 libffi 3.3 he6710b0_2 libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.5.0 h14aa051_19 conda-forge libgfortran4 7.5.0 h14aa051_19 conda-forge libgit2 1.0.1 h0b03e73_1 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 8_openblas conda-forge libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.1.0 hc3755c2_3 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxml2 2.9.10 h68273f3_2 conda-forge lz4-c 1.9.2 he1b5a44_3 conda-forge make 4.3 hd18ef5c_1 conda-forge ncurses 6.2 he6710b0_1 openssl 1.1.1h h516909a_0 conda-forge pango 1.42.4 h7062337_4 conda-forge pcre 8.44 he1b5a44_0 conda-forge pcre2 10.35 h279444b_1 conda-forge pip 19.3.1 py38_0 pixman 0.38.0 h516909a_1003 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pycosat 0.6.3 py38h7b6447c_1 pycparser 2.20 py_2 pyopenssl 19.1.0 pyhd3eb1b0_1 pysocks 1.7.1 py38h06a4308_0 python 3.8.5 h7579374_1 python_abi 3.8 2_cp38 conda-forge r 4.0 r40hd8ed1ab_1004 conda-forge r-askpass 1.1 r40hcdcec82_2 conda-forge r-assertthat 0.2.1 r40hc72bb7e_2 conda-forge r-backports 1.2.0 r40h9e2df91_0 conda-forge r-base 4.0.2 he766273_1 conda-forge r-base64enc 0.1_3 r40hcdcec82_1004 conda-forge r-boot 1.3_28 r40hc72bb7e_0 conda-forge r-brew 1.0_6 r40hc72bb7e_1003 conda-forge r-callr 3.7.0 r40hc72bb7e_0 conda-forge r-class 7.3_17 r40hcdcec82_1 conda-forge r-cli 3.0.1 r40hc72bb7e_0 conda-forge r-clipr 0.7.1 r40hc72bb7e_0 conda-forge r-cluster 2.1.0 r40h31ca83e_4 conda-forge r-codetools 0.2_18 r40hc72bb7e_0 conda-forge r-commonmark 1.7 r40hcdcec82_1002 conda-forge r-covr 3.5.1 r40h0357c0b_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 r40hcdcec82_1 conda-forge r-desc 1.3.0 r40hc72bb7e_0 conda-forge r-devtools 2.4.2 r40hc72bb7e_0 conda-forge r-digest 0.6.27 r40h1b71b39_0 conda-forge r-dt 0.18 r40hc72bb7e_0 conda-forge r-ellipsis 0.3.1 r40hcdcec82_0 conda-forge r-evaluate 0.14 r40hc72bb7e_2 conda-forge r-fansi 0.4.1 r40hcdcec82_1 conda-forge r-foreign 0.8_80 r40hcdcec82_0 conda-forge r-fs 1.5.0 r40h0357c0b_0 conda-forge r-gert 1.0.2 r40h9e2df91_0 conda-forge r-gh 1.3.0 r40hc72bb7e_0 conda-forge r-git2r 0.27.1 r40h7253d3a_0 conda-forge r-gitcreds 0.1.1 r40hc72bb7e_0 conda-forge r-glue 1.4.2 r40hcdcec82_0 conda-forge r-highr 0.9 r40hc72bb7e_0 conda-forge r-htmltools 0.5.0 r40h0357c0b_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 1.7.1 r40hcdcec82_0 conda-forge r-kernsmooth 2.23_18 r40h7679c2e_0 conda-forge r-knitr 1.33 r40hc72bb7e_0 conda-forge r-later 1.1.0.1 r40h0357c0b_0 conda-forge r-lattice 0.20_41 r40hcdcec82_2 conda-forge r-lazyeval 0.2.2 r40hcdcec82_2 conda-forge r-lifecycle 0.2.0 r40h6115d3f_1 conda-forge r-magrittr 2.0.1 r40h9e2df91_1 conda-forge r-markdown 1.1 r40hcdcec82_1 conda-forge r-mass 7.3_53 r40hcdcec82_0 conda-forge r-matrix 1.2_18 r40h7fa42b6_3 conda-forge r-memoise 1.1.0 r40h6115d3f_1004 conda-forge r-mgcv 1.8_33 r40h7fa42b6_0 conda-forge r-mime 0.9 r40hcdcec82_1 conda-forge r-nlme 3.1_150 r40h31ca83e_0 conda-forge r-nnet 7.3_14 r40hcdcec82_1 conda-forge r-openssl 1.4.3 r40he5c4762_0 conda-forge r-pkgbuild 1.2.0 r40hc72bb7e_0 conda-forge r-pkgload 1.1.0 r40h0357c0b_0 conda-forge r-praise 1.0.0 r40hc72bb7e_1004 conda-forge r-prettyunits 1.1.1 r40hc72bb7e_1 conda-forge r-processx 3.4.4 r40hcdcec82_0 conda-forge r-promises 1.1.1 r40h0357c0b_0 conda-forge r-ps 1.4.0 r40h0eb13af_0 conda-forge r-purrr 0.3.4 r40hcdcec82_1 conda-forge r-r6 2.5.0 r40hc72bb7e_0 conda-forge r-rappdirs 0.3.1 r40hcdcec82_1004 conda-forge r-rcmdcheck 1.3.3 r40hc72bb7e_3 conda-forge r-rcpp 1.0.5 r40he524a50_0 conda-forge r-recommended 4.0 r40hd8ed1ab_1004 conda-forge r-remotes 2.4.0 r40hc72bb7e_0 conda-forge r-rex 1.2.0 r40hc72bb7e_1 conda-forge r-rlang 0.4.8 r40h9e2df91_0 conda-forge r-roxygen2 7.1.1 r40h0357c0b_0 conda-forge r-rpart 4.1_15 r40hcdcec82_2 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-spatial 7.3_12 r40hcdcec82_1 conda-forge r-stringi 1.5.3 r40h604b29c_0 conda-forge r-stringr 1.4.0 r40hc72bb7e_2 conda-forge r-survival 3.2_7 r40hcdcec82_0 conda-forge r-sys 3.4 r40hcdcec82_0 conda-forge r-testthat 2.3.2 r40h0357c0b_1 conda-forge r-usethis 2.0.1 r40hc72bb7e_0 conda-forge r-whisker 0.4 r40hc72bb7e_1 conda-forge r-withr 2.4.2 r40hc72bb7e_0 conda-forge r-xfun 0.19 r40h9e2df91_0 conda-forge r-xml2 1.3.2 r40h0357c0b_1 conda-forge r-xopen 1.0.0 r40hc72bb7e_1003 conda-forge r-yaml 2.2.1 r40hcdcec82_1 conda-forge r-zip 2.1.1 r40hcdcec82_0 conda-forge readline 8.0 h7b6447c_0 requests 2.24.0 py_0 ruamel_yaml 0.15.87 py38h7b6447c_1 sed 4.8 he412f7d_0 conda-forge setuptools 50.3.1 py38h06a4308_1 six 1.15.0 py38h06a4308_0 sqlite 3.33.0 h62c20be_0 tk 8.6.10 hbc83047_0 tktable 2.10 hb7b940f_3 conda-forge tqdm 4.51.0 pyhd3eb1b0_0 urllib3 1.25.11 py_0 wheel 0.35.1 pyhd3eb1b0_0 xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.10 h516909a_0 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.12 h36c2ea0_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xz 5.2.5 h7b6447c_0 yaml 0.2.5 h7b6447c_0 zlib 1.2.11 h7b6447c_3 zstd 1.4.5 h6597ccf_2 conda-forge root@3f49d12504a3:/# R ```


Details about conda and system ( conda info ):

``` root@3f49d12504a3:/# conda info active environment : None user config file : /root/.condarc populated config files : conda version : 4.10.3 conda-build version : not installed python version : 3.8.5.final.0 virtual packages : __linux=4.15.0=0 __glibc=2.31=0 __unix=0=0 __archspec=1=x86_64 base environment : /opt/miniconda (writable) conda av data dir : /opt/miniconda/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /opt/miniconda/pkgs /root/.conda/pkgs envs directories : /opt/miniconda/envs /root/.conda/envs platform : linux-64 user-agent : conda/4.10.3 requests/2.24.0 CPython/3.8.5 Linux/4.15.0-142-generic ubuntu/20.04.2 glibc/2.31 UID:GID : 0:0 netrc file : None offline mode : False ```
jdblischak commented 3 years ago

@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 halted

Environment (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 ```
bainadeashish commented 3 years ago

no value of GIT_URL is correct, same is working fine with cran devtools but fails in r-devtools conda. @jdblischak

jdblischak commented 3 years ago

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 deactivate
bainadeashish commented 3 years ago

@jdblischak let me try & will update accordingly. Thanks alot

bainadeashish commented 3 years ago

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.

jdblischak commented 3 years ago

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:

  1. 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 run conda install git.

  2. 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 with install_gitlab()

  3. 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 it

    git clone https://gitlab+deploy-token-49:MVJMoJQbGThZbdzEb@GIT_REPO.git
Rscript -e 'devtools::install("GIT_REPO")'