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Question: Illumina Methylation Manifest Install
0
gravatar for julieumn
9 months ago by
julieumn0
julieumn0 wrote:

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

 

How do I get the package to install correctly?

ADD COMMENTlink modified 9 months ago • written 9 months ago by julieumn0

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"


biocLite("IlluminaHumanMethylation450kmanifest", lib="/pathToYourLibrary")
ADD REPLYlink modified 9 months ago • written 9 months ago by shepherl ♦♦ 1.1k
Answer: Illumina Methylation Manifest Install
0
gravatar for julieumn
9 months ago by
julieumn0
julieumn0 wrote:

Hi,  I am using Windows10.  Here is my session info. 

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.30.0

loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 
ADD COMMENTlink written 9 months ago by julieumn0

Can you please provide the output from:

.libPaths() 
biocLite("IlluminaHumanMethylation450kmanifest")

Is your desired installation directory found in the results from .libPaths()? Is this a shared computer (in a lab) or a personal computer?

ADD REPLYlink modified 9 months ago • written 9 months ago by shepherl ♦♦ 1.1k
Answer: Illumina Methylation Manifest Install
0
gravatar for julieumn
9 months ago by
julieumn0
julieumn0 wrote:
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

 

ADD COMMENTlink written 9 months ago by julieumn0
Answer: Illumina Methylation Manifest Install
0
gravatar for julieumn
9 months ago by
julieumn0
julieumn0 wrote:

Thanks for all your help - seems all my issues were fixed with 'install.packages("package name", dependencies = TRUE)'

ADD COMMENTlink written 9 months ago by julieumn0
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