I was trying to create a new conda environment with r-base=3.6.3 and rstudio at the same time and it didn't work for me
That's the command line I wrote
conda create -n test6 -c conda-forge r-base=3.6.3 rstudio r-seurat=3.2.3
and that was the error I got
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package r-xtable conflicts for:
rstudio -> r-shiny[version='>=1.0'] -> r-xtable
rstudio -> r-xtable[version='>=1.7']
Package r-htmltools conflicts for:
rstudio -> r-htmltools[version='>=0.3.5']
rstudio -> r-htmlwidgets[version='>=0.6'] -> r-htmltools[version='>=0.3.6|>=0.3|>=0.5.0.9001|>=0.4.0']
Package r-r6 conflicts for:
rstudio -> r-httpuv[version='>=1.3.3'] -> r-r6
rstudio -> r-r6[version='>=2.0']
Package r-rjsonio conflicts for:
rstudio -> r-rsconnect[version='>=0.8.5'] -> r-rjsonio
rstudio -> r-rjsonio[version='>=1.0|>=1.3']
Package r-sourcetools conflicts for:
rstudio -> r-shiny[version='>=1.0'] -> r-sourcetools
rstudio -> r-sourcetools[version='>=0.1.5']
Package gcc_linux-64 conflicts for:
r-base=3.6.3 -> gfortran_linux-64=9 -> gcc_linux-64[version='10.3.0|10.3.0|11.1.0|11.1.0|11.2.0|9.3.0|9.3.0|9.3.0|9.3.0|9.3.0|9.3.0|9.3.0|9.3.0|9.3.0|9.3.0|9.3.0|9.4.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.5.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.3.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|7.2.0|8.5.0|8.4.0|8.4.0|8.4.0|8.4.0|8.4.0|8.4.0|8.4.0|8.4.0|8.4.0|8.4.0|8.4.0|8.2.0|8.2.0',build='h218040c_2|he201b7d_30|h963c828_27|h963c828_28|hd6b9e8f_30|hd6b9e8f_31|hd6b9e8f_32|h87d5063_1|h22f992b_7|h6f34251_8|h196ecd4_10|h4118e58_11|hd763dfe_12|hf1c97a4_14|19|26|h553295d_3|h553295d_7|h553295d_10|h553295d_13|h553295d_14|h553295d_17|h553295d_18|h09487f9_19|h09487f9_20|ha781d05_22|hf34d7eb_26|hf34d7eb_27|he2a3fca_29|h47867f9_32|hc39de41_1|h97fdae6_1|h1ee779e_30|h70133e4_23|h70133e4_25|h44160b2_28|hf25ea35_33|h391b98a_1|h391b98a_0|hf25ea35_32|hf25ea35_31|hf25ea35_30|h7247604_29|h44160b2_27|h44160b2_26|h39a9532_1|h97fdae6_0|hc39de41_0|h47867f9_33|h47867f9_31|h47867f9_30|hf34d7eb_28|hcce3721_25|ha781d05_23|ha781d05_21|h8f34230_30|h553295d_16|h553295d_15|h553295d_12|h553295d_11|h553295d_9|h553295d_0|h553295d_8|h553295d_6|h553295d_2|h550dcbe_27|25|haf1f6fa_15|h217957b_13|h60973fd_9|h29fd5c9_3|hecb3f9c_2|hc7b1ceb_1|hd6b9e8f_33|haf9d283_29|h963c828_26|hf74bdac_25|hf74bdac_23|h218040c_3']
r-base=3.6.3 -> gcc_linux-64[version='>=7|>=9']
r-seurat=3.2.3 -> r-base[version='>=3.6,<3.7.0a0'] -> gcc_linux-64[version='7.*|>=7|>=9']
Package r-stringr conflicts for:
rstudio -> r-stringr[version='>=0.6']
rstudio -> r-evaluate[version='>=0.8'] -> r-stringr[version='>=0.6.2|>=1.2.0|>=1.3.1|>=1.3.0|>=1.1.0']
Package r-shiny conflicts for:
rstudio -> r-miniui[version='>=0.1.1'] -> r-shiny[version='0.12.2|>=0.13.2|>=0.13|>=1.0.1|>=1.2.0|>=1.1.0|>=1.0.5|>=1.0.3|>=0.14.2']
rstudio -> r-shiny[version='>=1.0']
Package r-digest conflicts for:
rstudio -> r-digest[version='>=0.6']
rstudio -> r-htmltools[version='>=0.3.5'] -> r-digest[version='>=0.6.25']
Package r-jsonlite conflicts for:
rstudio -> r-htmlwidgets[version='>=0.6'] -> r-jsonlite[version='0.9.17|>=0.9.16|>=1.4|>=1.5|>=1.1|>=0.9.22']
rstudio -> r-jsonlite[version='>=0.9.19']
Package r-base64enc conflicts for:
rstudio -> r-base64enc[version='>=0.1-3']
rstudio -> r-htmltools[version='>=0.3.5'] -> r-base64enc
Package r-base conflicts for:
rstudio -> r-base64enc[version='>=0.1-3'] -> r-base[version='3.1.3.*|3.2.0.*|3.2.1.*|3.2.2.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=4.0,<4.1.0a0|>=4.1,<4.2.0a0|>=3.5.1,<3.5.2.0a0|>=3.5.0,<3.5.1.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0|3.4.1|>=3.4.2|>=3.3.2|>=3.3.1|3.2.2']
r-base=3.6.3
r-seurat=3.2.3 -> r-base[version='>=3.6,<3.7.0a0|>=4.0,<4.1.0a0']
r-seurat=3.2.3 -> r-cluster -> r-base[version='3.1.3.*|3.2.0.*|3.2.1.*|3.2.2.*|3.3.1.*|3.3.2.*|3.4.1.*|>=3.4.1,<3.4.2.0a0|>=3.5,<3.6.0a0|>=4.1,<4.2.0a0|>=3.5.1,<3.5.2.0a0|>=3.5.0,<3.5.1.0a0|>=3.4.3,<3.4.4.0a0|>=3.4.2,<3.4.3a0']
Package r-htmlwidgets conflicts for:
rstudio -> r-profvis[version='>=0.3.2'] -> r-htmlwidgets[version='>=0.3.2']
rstudio -> r-htmlwidgets[version='>=0.6']
Package openssl conflicts for:
rstudio -> qt=5.6 -> openssl[version='1.0.*|>=1.0.2p,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.1.1c,<1.1.2a|>=1.1.1a,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.1.1k,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1b,<1.1.2a']
r-base=3.6.3 -> curl -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.1.1k,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1a,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.0.2n,<1.0.3a']
Package r-httpuv conflicts for:
rstudio -> r-httpuv[version='>=1.3.3']
rstudio -> r-shiny[version='>=1.0'] -> r-httpuv[version='>=1.3.5|>=1.4.3|>=1.4.4|>=1.5.0|>=1.5.2']
Package r-plyr conflicts for:
rstudio -> r-essentials[version='>=1.7.0'] -> r-plyr[version='1.8.3|>=1.8.4']
r-seurat=3.2.3 -> r-cowplot -> r-plyr[version='>=1.8.0|>=1.8.2']
Package r-rcpp conflicts for:
rstudio -> r-rcpp[version='>=0.11.5']
rstudio -> r-haven[version='>=0.2.0'] -> r-rcpp[version='>=0.11.0|>=0.11.4|>=0.12.11|>=0.12.0.5|>=0.12.18|>=0.12.12|>=0.11.6|>=0.11.4.6']
Package r-mime conflicts for:
rstudio -> r-mime[version='>=0.3']
rstudio -> r-mongolite[version='>=0.8'] -> r-mimeThe following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.27=0
- feature:|@/linux-64::__glibc==2.27=0
- r-seurat=3.2.3 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- rstudio -> libgcc-ng[version='>=7.2.0'] -> __glibc[version='>=2.17']
Your installed version is: 2.27
It works fine if I tried creating a new environment with r-base only or rstudio without the conda-forge channel. They just don't work together on the same environment.
the conda-forge channel doesn't have rstudio, so rstudio will be installed through the r channel. I can't use the r channel because the most recent r-base on this channel is 3.6.1 and seurat package works with at least r-base 3.6.3
