I recently removed several R packages (using remove.packages()), and re-installed their newest versions. I tried to re-install the library grid using the following syntax:
url <- "https://cran.r-project.org/src/contrib/Archive/grid/grid_0.7-4.tar.gz"
pkgFile <- "grid_0.7-4.tar.gz"
download.file(url = url, destfile = pkgFile)
install.packages(pkgs=pkgFile, type="source", repos=NULL)
unlink(pkgFile)
I received the following warnings and errors:
Error : Invalid DESCRIPTION file
Invalid package name.
This is the name of a base package.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ERROR: installing package DESCRIPTION failed for package ‘grid’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/grid’
Warning in install.packages :
installation of package ‘/Users/lindz/RNASeqVisualization/grid_0.7-4.tar.gz’ had non-zero exit status
It seems that grid is now part of base R, so I temporarily moved on. However, upon reinstalling the package ggplot2 using:
install.packages("ggplot2")
I received the following warnings:
Warning in install.packages :
URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': status was '400 Bad Request'
Warning in install.packages :
URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot download all files
Warning in install.packages :
URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES.gz': status was '400 Bad Request'
Warning in install.packages :
URL 'https://R-Forge.R-project.org/src/contrib/PACKAGES': status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/src/contrib:
cannot download all files
Warning in install.packages :
dependency ‘grid’ is not available
Warning in install.packages :
unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/macosx/mavericks/contrib/3.3:
Line starting '<!DOCTYPE html> ...' is malformed!
Warning in install.packages :
URL 'http://www.omegahat.net/R/bin/macosx/mavericks/contrib/3.3/PACKAGES.gz': status was '404 Not Found'
Warning in install.packages :
URL 'http://www.omegahat.net/R/bin/macosx/mavericks/contrib/3.3/PACKAGES': status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://www.omegahat.net/R/bin/macosx/mavericks/contrib/3.3:
cannot download all files
Warning in install.packages :
URL 'https://R-Forge.R-project.org/bin/macosx/mavericks/contrib/3.3/PACKAGES.gz': status was '400 Bad Request'
Warning in install.packages :
URL 'https://R-Forge.R-project.org/bin/macosx/mavericks/contrib/3.3/PACKAGES': status was '400 Bad Request'
Warning in install.packages :
unable to access index for repository https://R-Forge.R-project.org/bin/macosx/mavericks/contrib/3.3:
cannot download all files
Warning in install.packages :
URL 'https://www.rforge.net/bin/macosx/mavericks/contrib/3.3/PACKAGES.gz': status was '404 Not Found'
Warning in install.packages :
URL 'https://www.rforge.net/bin/macosx/mavericks/contrib/3.3/PACKAGES': status was '404 Not Found'
Warning in install.packages :
unable to access index for repository https://www.rforge.net/bin/macosx/mavericks/contrib/3.3:
cannot download all files
When I then ran:
library(ggplot2)
I received the errors:
Error : package ‘grid’ does not have a namespace
Error: package or namespace load failed for ‘ggplot2’
I am unsure what to do at this point. I have seen similar posts (R error package grid does not have a namespace), but their solutions do not work for mine. I do not have grid saved in my any Library, since I already de-installed it (using remove.packages()).
My sessionInfo() is as follows:
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggenealogy_0.2.0
loaded via a namespace (and not attached):
[1] rsconnect_0.4.3 tools_3.3.1
Any advice would be greatly appreciated!
grid is a red herring, it comes with R, no need to try and reinstall it (else update R itself).
ggplot2 you should install from CRAN or github, not R-forge. Try a CRAN repository.