I am having a difficult time using biocLite to install IlluminaMethylationManifest. I received this message:
> biocLite("IlluminaMethylationManifest")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘IlluminaMethylationManifest’
installation path not writeable, unable to update packages: MASS, survival
Old packages: 'BiocParallel'
Update all/some/none? [a/s/n]:
So I found the download and removed the .tar.gz and then moved the files to my R library but that gave me this:
> library(IlluminaHumanMethylation450kmanifest)
Error in library(IlluminaHumanMethylation450kmanifest) :
‘IlluminaHumanMethylation450kmanifest’ is not a valid installed package
What OS are you using? Could you share your sessionInfo()
Are you using an R installation that was installed by root? Even though you moved the tar.gz file you would still have to install the package for R to find it.
You can see what directories R is trying to install the package to .libPaths(). You should make sure your path to your library is displayed there. If not you can add it .libPaths("/pathToYourLibrary")
If you want to install the library in a specific location you could use the lib argument, Note also that in your first example you were installing "IlluminaMethylationManifest" and it should be "IlluminaHumanMethylation450kmanifest"
libPaths()
[1] "C:/Users/adm-jmeyer/Documents/R/win-library/3.5" "C:/Program Files/R/R-3.5.0/library"
> biocLite("IlluminaHumanMethylation450kmanifest")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘IlluminaHumanMethylation450kmanifest’
installing the source package ‘IlluminaHumanMethylation450kmanifest’
trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz'
Content type 'application/x-gzip' length 8726870 bytes (8.3 MB)
downloaded 8.3 MB
* installing *source* package 'IlluminaHumanMethylation450kmanifest' ...
** data
*** moving datasets to lazyload DB
** inst
** help
*** installing help indices
converting help for package 'IlluminaHumanMethylation450kmanifest'
finding HTML links ... done
IlluminaHumanMethylation450kmanifest html
** building package indices
** testing if installed package can be loaded
*** arch - i386
Error: package or namespace load failed for 'bumphunter' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called 'stringi'
Error : package 'bumphunter' could not be loaded
Error: loading failed
Execution halted
*** arch - x64
Error: package or namespace load failed for 'bumphunter' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called 'stringi'
Error : package 'bumphunter' could not be loaded
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing 'C:/Users/adm-jmeyer/Documents/R/win-library/3.5/IlluminaHumanMethylation450kmanifest'
* restoring previous 'C:/Users/adm-jmeyer/Documents/R/win-library/3.5/IlluminaHumanMethylation450kmanifest'
In R CMD INSTALL
The downloaded source packages are in
‘C:\Users\adm-jmeyer\AppData\Local\Temp\RtmpApeyX4\downloaded_packages’
installation path not writeable, unable to update packages: MASS, survival
Old packages: 'BiocParallel'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
BiocParallel 1.13.1 1.14.0 TRUE
Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/BiocParallel_1.13.1.zip'
Content type 'application/zip' length 2643018 bytes (2.5 MB)
downloaded 2.5 MB
package ‘BiocParallel’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\adm-jmeyer\AppData\Local\Temp\RtmpApeyX4\downloaded_packages
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘IlluminaHumanMethylation450kmanifest’ had non-zero exit status
Have installed bumphunter. This is the message with bumphunter:
> biocLite("bumphunter")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘bumphunter’
trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/bumphunter_1.22.0.zip'
Content type 'application/zip' length 4691656 bytes (4.5 MB)
downloaded 4.5 MB
package ‘bumphunter’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\adm-jmeyer\AppData\Local\Temp\RtmpApeyX4\downloaded_packages
installation path not writeable, unable to update packages: MASS, survival
Old packages: 'BiocParallel'
Update all/some/none? [a/s/n]:
n
Hello,
What OS are you using? Could you share your
sessionInfo()Are you using an R installation that was installed by root? Even though you moved the tar.gz file you would still have to install the package for R to find it.
You can see what directories R is trying to install the package to
.libPaths(). You should make sure your path to your library is displayed there. If not you can add it.libPaths("/pathToYourLibrary")If you want to install the library in a specific location you could use the lib argument, Note also that in your first example you were installing "IlluminaMethylationManifest" and it should be "IlluminaHumanMethylation450kmanifest"