Question: Problem to install "flowClust"
0
gravatar for cr
2.4 years ago by
cr0
cr0 wrote:

Hi,

I try to install the package "flowClust" but I can't and I have this warning message " In install.packages(pkgs = doing, lib = lib, ...) : installation of package 'flowClust' had non-zero exit status".

I have done this : source("http://bioconductor.org/biocLite.R")
                         biocLite("flowClust", type = "source")

My version is R3.2.4

Thanks,

Céline

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by cr0

If you are using Windows, do you really want to install the package from source?

The error message seems too short to me, and you should your full sessionInfo() in order to get meaningful help.
 

ADD REPLYlink written 2.4 years ago by SamGG180

Thank you for your answer.

I unsuccessfully tried : install.package("flowClust") and to install from the zip file without success. That's why i tried from the source.

I have got this Warning message:
package 'flowClust' is not available (for R version 3.2.4 Revised)

 

With SessionInfo() :

sessionInfo()
R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

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

other attached packages:
 [1] BiocInstaller_1.20.3 flowViz_1.34.1       lattice_0.20-34      flowCore_1.36.9      corrplot_0.77        reshape2_1.4.2      
 [7] tidyr_0.6.0          calibrate_1.7.2      MASS_7.3-45          rj_2.0.4-2          

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'robustbase' is missing or broken

When I run this, I have no problem:

> pdb <- available.packages()
> deps <- tools::package_dependencies(packages = "robustbase", pdb)
> deps
$robustbase
[1] "stats"    "graphics" "utils"    "methods"  "DEoptimR"

ADD REPLYlink written 2.4 years ago by cr0

It's a Bioconductor package so from the package landing page

source("https://bioconductor.org/biocLite.R")
biocLite("flowClust")
ADD REPLYlink written 2.4 years ago by Martin Morgan ♦♦ 23k

Exactly, any Bioc package installed with "install.package()" will lead to a "not available" error.

So, do try Martin's command please.

ADD REPLYlink written 2.4 years ago by SamGG180
Answer: Problem to install "flowClust"
0
gravatar for cr
2.4 years ago by
cr0
cr0 wrote:

Thank you Martin and SamGG.

In fact I reinstalled R software with the latest version 3.3.2 and run

source("https://bioconductor.org/biocLite.R")
biocLite("flowClust")

And now everything is ok.

ADD COMMENTlink written 2.4 years ago by cr0
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