Question: Error while installing Phyloseq using biocLite
1
gravatar for khp
12 months ago by
khp30
khp30 wrote:

Hello, 


I'm trying to install phyloseq and get this error: 

source('https://bioconductor.org/biocLite.R')

#Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help

 biocLite('phyloseq')
Error: 'no packages in repository (no internet connection?)' while trying https://bioconductor.org/packages/3.7/bioc

I tried the way you suggested here: C: Error using biocLite, but get the same error.

 

 options(BioC_mirror="http://bioconductor.org")
> biocLite("org.Hs.eg.db")
Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/3.7/bioc

I do have internet connection. I would appreciate your help with this. 

 

Other information:

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

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 dada2_1.9.2          Rcpp_0.12.19     

ADD COMMENTlink written 12 months ago by khp30

Can you visit http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES in your browser? What about in an R session source("http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES") ?

ADD REPLYlink written 12 months ago by Martin Morgan ♦♦ 23k
1

In my browser the link goes to a page that begins with 

Package: affxparser
Version: 1.52.0
Depends: R (>= 2.14.0)
Suggests: R.oo (>= 1.20.0), R.utils (>= 2.4.0), AffymetrixDataTestFiles
License: LGPL (>= 2)
Archs: i386, x64

 

and goes on to list many other packages. 

 

In my R session, when I type 

source("http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES")

I get:

Error in source("http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES") : 
  http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES:2:14: unexpected numeric constant
1: Package: a4
2: Version: 1.28.0
                ^

:( 

 

EDIT: The ^ is actually under the period between 28 and 0. If it helps...

ADD REPLYlink modified 12 months ago • written 12 months ago by khp30

seems like you _do_ have internet access, including from within R. Can you try explicitly calling BiocManager::biocLite("org.Hs.eg.db") ? I'm not really sure what is going on...

ADD REPLYlink modified 12 months ago • written 12 months ago by Martin Morgan ♦♦ 23k
1

> BiocManager::biocLite("org.Hs.eg.db")
Error in loadNamespace(name) : there is no package called ‘BiocManager’
> biocLite("org.Hs.eg.db")
Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/3.7/bioc

 

ADD REPLYlink written 12 months ago by khp30

Argh, I meant BiocInstaller::biocLite("org.Hs.eg.db")

ADD REPLYlink written 12 months ago by Martin Morgan ♦♦ 23k

 BiocInstaller::biocLite("org.Hs.eg.db")
Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/3.7/bioc

:( Sorry, this is my first time doing this.... 

 

EDIT: 

I also tried this method, but it didn't work:

 source("https://raw.githubusercontent.com/joey711/phyloseq/master/inst/scripts/installer.R",
+        local = TRUE)
Installing the release version from BioC
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/3.7/bioc

Could it be possible that the latest bioconductor version does not have the phyloseq package yet? 

 

PS: I have reached the limit of the number of posts allowed. So I'm unable to make new posts right now. I did try what you suggested and this is what I got:

> contrib.url("http://bioconductor.org/packages/3.7/bioc")
[1] "http://bioconductor.org/packages/3.7/bioc/src/contrib"
> head(available.packages(contrib.url("http://bioconductor.org/packages/3.7/bioc")))
Warning: unable to access index for repository http://bioconductor.org/packages/3.7/bioc/src/contrib:
  cannot open destfile 'C:\Users\khp\AppData\Local\Temp\Rtmpk7XwQ3\file79d6884a6a55', reason 'No such file or directory'
     Package Version Priority Depends Imports LinkingTo Suggests Enhances License License_is_FOSS License_restricts_use OS_type Archs MD5sum
     NeedsCompilation File Repository

 

I checked that this C:\Users\khp\AppData\Local\Temp exists, but the other folder and file in the path does not exist. 

ADD REPLYlink modified 12 months ago • written 12 months ago by khp30
1

phyloseq is available in that version of Bioconductor.

Try

contrib.url("http://bioconductor.org/packages/3.7/bioc")

and

head(available.packages(contrib.url("http://bioconductor.org/packages/3.7/bioc")))
ADD REPLYlink written 12 months ago by Martin Morgan ♦♦ 23k

I tried to up-vote your question & answers so you have more credibility... what does getOption("pkgType") say? Does it help to put options(pkgType = "win.binary") and then try the available.packages() command again?

ADD REPLYlink modified 12 months ago • written 12 months ago by Martin Morgan ♦♦ 23k

Thanks. This is what I get:

 getOption("pkgType")
[1] "both"
> options(pkgType="win.binary")
> contrib.url("http://bioconductor.org/packages/3.7/bioc")
[1] "http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5"
> head(available.packages(contrib.url("http://bioconductor.org/packages/3.7/bioc")))
Warning: unable to access index for repository http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5:
  cannot open destfile 'C:\Users\Kaumudi\AppData\Local\Temp\Rtmpk7XwQ3\file79d684df923b8', reason 'No such file or directory'
     Package Version Priority Depends Imports LinkingTo Suggests Enhances License License_is_FOSS License_restricts_use OS_type Archs MD5sum
     NeedsCompilation File Repository

 

ADD REPLYlink written 12 months ago by khp30
1

I believe the error is coming when R tries to download the file http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES (which exists) via the equivalent of

fl = "http://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES"
dest = tempfile()
download.file(fl, dest)

Does that fail for you? What is getOption("download.file.method") ?

ADD REPLYlink written 12 months ago by Martin Morgan ♦♦ 23k

Yay!! This worked. I did what you just suggested and then did

source('https://bioconductor.org/biocLite.R') 

 biocLite('phyloseq')

and everything was installed. I must also add that I restarted the machine before doing this. 

Thank you Martin for your patience with all my questions! You have been most helpful :-) 

ADD REPLYlink written 12 months ago by khp30
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