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Proteomicslab57357 / UniprotR

Retrieving Information of Proteins from Uniprot
GNU General Public License v3.0
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Installation/dependency issues #10

Closed joegeorgeson closed 3 years ago

joegeorgeson commented 3 years ago

Hi UniprotR devs,

Just wanted to make you aware of this issue. I have (unsuccessfully) tried installing to 3.6.1 and 4.0.3 and get dependency errors.

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin19.6.0 (64-bit)
Running under: macOS Catalina 10.15.7
>install.packages("UniprotR")
.
.
.
ERROR: compilation failed for package ‘graphlayouts’
* removing ‘/usr/local/lib/R/4.0/site-library/graphlayouts’
ERROR: dependency ‘graphlayouts’ is not available for package ‘ggraph’
* removing ‘/usr/local/lib/R/4.0/site-library/ggraph’
ERROR: dependency ‘ggraph’ is not available for package ‘enrichplot’
* removing ‘/usr/local/lib/R/4.0/site-library/enrichplot’
ERROR: dependencies ‘enrichplot’, ‘ggraph’, ‘reactome.db’ are not available for package ‘ReactomePA’
* removing ‘/usr/local/lib/R/4.0/site-library/ReactomePA’

The downloaded source packages are in
    ‘/private/var/folders/t5/l5xhh29x4kx6j5zb4q38_jyw0000gn/T/Rtmp0ZqPJ9/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘graphlayouts’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘ggraph’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘enrichplot’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘ReactomePA’ had non-zero exit status
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Catalina 10.15.7
>install.packages("UniprotR")
.
.
.
Warning in install.packages :
  installation of package ‘magick’ had non-zero exit status
ERROR: dependency ‘RcppArmadillo’ is not available for package ‘conquer’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/conquer’
Warning in install.packages :
  installation of package ‘conquer’ had non-zero exit status
* installing *source* package ‘broom’ ...
** package ‘broom’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘tidyr’ 0.8.3 is being loaded, but >= 1.0.0 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘broom’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/broom’
Warning in install.packages :
  installation of package ‘broom’ had non-zero exit status
ERROR: dependency ‘farver’ is not available for package ‘scales’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/scales’
Warning in install.packages :
  installation of package ‘scales’ had non-zero exit status
ERROR: dependency ‘broom’ is not available for package ‘pbkrtest’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/pbkrtest’
Warning in install.packages :
  installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency ‘conquer’ is not available for package ‘quantreg’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/quantreg’
Warning in install.packages :
  installation of package ‘quantreg’ had non-zero exit status
ERROR: dependency ‘broom’ is not available for package ‘modelr’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/modelr’
Warning in install.packages :
  installation of package ‘modelr’ had non-zero exit status
ERROR: dependencies ‘isoband’, ‘scales’ are not available for package ‘ggplot2’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/ggplot2’
Warning in install.packages :
  installation of package ‘ggplot2’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘quantreg’, ‘maptools’, ‘rio’ are not available for package ‘car’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/car’
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status
ERROR: dependencies ‘ggplot2’, ‘scales’ are not available for package ‘ggrepel’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/ggrepel’
Warning in install.packages :
  installation of package ‘ggrepel’ had non-zero exit status
ERROR: dependencies ‘scales’, ‘ggplot2’ are not available for package ‘ggsci’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/ggsci’
Warning in install.packages :
  installation of package ‘ggsci’ had non-zero exit status
ERROR: dependencies ‘ggplot2’, ‘scales’ are not available for package ‘cowplot’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/cowplot’
Warning in install.packages :
  installation of package ‘cowplot’ had non-zero exit status
ERROR: dependency ‘ggplot2’ is not available for package ‘ggsignif’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/ggsignif’
Warning in install.packages :
  installation of package ‘ggsignif’ had non-zero exit status
ERROR: dependencies ‘ggplot2’, ‘scales’ are not available for package ‘plotly’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/plotly’
Warning in install.packages :
  installation of package ‘plotly’ had non-zero exit status
ERROR: dependencies ‘broom’, ‘ggplot2’, ‘lubridate’, ‘modelr’ are not available for package ‘tidyverse’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/tidyverse’
Warning in install.packages :
  installation of package ‘tidyverse’ had non-zero exit status
ERROR: dependencies ‘ggplot2’, ‘scales’ are not available for package ‘alakazam’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/alakazam’
Warning in install.packages :
  installation of package ‘alakazam’ had non-zero exit status
ERROR: dependencies ‘broom’, ‘car’ are not available for package ‘rstatix’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/rstatix’
Warning in install.packages :
  installation of package ‘rstatix’ had non-zero exit status
ERROR: dependencies ‘ggplot2’, ‘plotly’ are not available for package ‘gprofiler2’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/gprofiler2’
Warning in install.packages :
  installation of package ‘gprofiler2’ had non-zero exit status
ERROR: dependencies ‘ggplot2’, ‘ggrepel’, ‘ggsci’, ‘cowplot’, ‘ggsignif’, ‘scales’, ‘rstatix’ are not available for package ‘ggpubr’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/ggpubr’
Warning in install.packages :
  installation of package ‘ggpubr’ had non-zero exit status
ERROR: dependencies ‘scales’, ‘magick’, ‘ggplot2’, ‘tidyverse’, ‘ggpubr’, ‘alakazam’, ‘ReactomePA’, ‘gprofiler2’ are not available for package ‘UniprotR’
* removing ‘/usr/local/anaconda3/envs/rstudio_UniprotR/lib/R/library/UniprotR’
Warning in install.packages :
  installation of package ‘UniprotR’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/t5/l5xhh29x4kx6j5zb4q38_jyw0000gn/T/RtmpRJ1bCd/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
MohmedSoudy commented 3 years ago

Thank you for your effort, i can see that the package raise an error in CRAN checks on mac-os system, this issue due to ReactomePA package from bioconductor we will remove this package in the next update.