Error in updating Seurat packages

[hnglong2610]

Good morning everyone,

I am a newbie in R. I am using R4.0.5 for scRNA-seq analysis. Recently I tried to update Seurat packages (Tools/Check for Package updates/...) but it appeared errors as below

installing source package 'tinytex' ...
** package 'tinytex' 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 'xfun' 0.30 is being loaded, but >= 0.48 is required
Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'tinytex'

• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/tinytex'
  Warning in install.packages :
  installation of package ‘tinytex’ had non-zero exit status
• installing source package 'knitr' ...
  ** package 'knitr' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** demo
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  namespace 'xfun' 0.30 is being loaded, but >= 0.48 is required
  Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
  Execution halted
  ERROR: lazy loading failed for package 'knitr'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/knitr'
  Warning in install.packages :
  installation of package ‘knitr’ had non-zero exit status
• installing source package 'spatstat.data' ...
  ** package 'spatstat.data' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  namespace 'spatstat.utils' 2.3-0 is being loaded, but >= 3.0.5 is required
  Calls: ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
  Execution halted
  ERROR: lazy loading failed for package 'spatstat.data'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/spatstat.data'
  Warning in install.packages :
  installation of package ‘spatstat.data’ had non-zero exit status
• installing source package 'future' ...
  ** package 'future' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** demo
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
  namespace 'parallelly' 1.31.0 is being loaded, but >= 1.38.0 is required
  Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
  Execution halted
  ERROR: lazy loading failed for package 'future'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/future'
  Warning in install.packages :
  installation of package ‘future’ had non-zero exit status
• installing source package 'lifecycle' ...
  ** package 'lifecycle' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  namespace 'rlang' 1.0.2 is being loaded, but >= 1.1.0 is required
  Calls: ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
  Execution halted
  ERROR: lazy loading failed for package 'lifecycle'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/lifecycle'
  Warning in install.packages :
  installation of package ‘lifecycle’ had non-zero exit status
  ERROR: dependency 'lifecycle' is not available for package 'gtable'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/gtable'
  Warning in install.packages :
  installation of package ‘gtable’ had non-zero exit status
  ERROR: dependency 'lifecycle' is not available for package 'stringr'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/stringr'
  Warning in install.packages :
  installation of package ‘stringr’ had non-zero exit status
  ERROR: dependency 'lifecycle' is not available for package 'bslib'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/bslib'
  Warning in install.packages :
  installation of package ‘bslib’ had non-zero exit status
  ERROR: dependency 'future' is not available for package 'future.apply'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/future.apply'
  Warning in install.packages :
  installation of package ‘future.apply’ had non-zero exit status
  ERROR: dependencies 'bslib', 'knitr', 'tinytex' are not available for package 'rmarkdown'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/rmarkdown'
  Warning in install.packages :
  installation of package ‘rmarkdown’ had non-zero exit status
  ERROR: dependency 'stringr' is not available for package 'fastDummies'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/fastDummies'
  Warning in install.packages :
  installation of package ‘fastDummies’ had non-zero exit status
  ERROR: dependencies 'gtable', 'lifecycle' are not available for package 'ggplot2'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/ggplot2'
  Warning in install.packages :
  installation of package ‘ggplot2’ had non-zero exit status
  ERROR: dependencies 'bslib', 'lifecycle' are not available for package 'shiny'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/shiny'
  Warning in install.packages :
  installation of package ‘shiny’ had non-zero exit status
  ERROR: dependencies 'knitr', 'rmarkdown' are not available for package 'htmlwidgets'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/htmlwidgets'
  Warning in install.packages :
  installation of package ‘htmlwidgets’ had non-zero exit status
  ERROR: dependencies 'ggplot2', 'gtable' are not available for package 'cowplot'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/cowplot'
  Warning in install.packages :
  installation of package ‘cowplot’ had non-zero exit status
  ERROR: dependency 'ggplot2' is not available for package 'ggridges'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/ggridges'
  Warning in install.packages :
  installation of package ‘ggridges’ had non-zero exit status
  ERROR: dependencies 'ggplot2', 'gtable' are not available for package 'patchwork'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/patchwork'
  Warning in install.packages :
  installation of package ‘patchwork’ had non-zero exit status
  ERROR: dependencies 'ggplot2', 'htmlwidgets' are not available for package 'plotly'
• removing 'C:/Users/Hien Hoang/Documents/R/win-library/4.0/plotly'
  Warning in install.packages :
  installation of package ‘plotly’ had non-zero exit status

Please help me to solve this problem!

Thank you.

[samuel-marsh]

Hi @hnglong2610,

Not member of dev team but hopefully can be helpful. Did you restart your R session before updating these packages? It seems some of the errors are due to packages being loaded already? If this still doesn't solve your issue you might want to try removing the packages with issues and then reinstalling them fresh from their newest versions.

Best,
Sam