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Question: Flowclust install probelms on Ubuntu
0
gravatar for gareth.howell
3.6 years ago by
United Kingdom
gareth.howell0 wrote:

Hi I am having an issue installing the flow cytometry package flowClust on my Ubuntu 14 system.

Other packages such as SamSPECTRAL install fine.

I get this error at the end of the install process which may help:

 

Commands:

source("http://bioconductor.org/biocLite.R")

biocLite("flowClust")

> library(flowClust)
Error in library(flowClust) : there is no package called ‘flowClust’
installing to /home/gareth/R/i686-pc-linux-gnu-library/3.1/flowClust/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: S3 methods ‘print.BayesFactor’, ‘summary.BayesFactor’, ‘plot.qrssvs’, ‘print.qrssvs’, ‘print.summary.qrssvs’, ‘summary.qrssvs’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) : 
  shared object ‘MCMCpack.so’ not found
ERROR: lazy loading failed for package ‘flowClust’
* removing ‘/home/gareth/R/i686-pc-linux-gnu-library/3.1/flowClust’
Warning in install.packages :
  installation of package ‘/home/gareth/Downloads/flowClust_3.6.0.tar.gz’ had non-zero exit status

 

SessionInfo() output:

R version 3.1.3 (2015-03-09)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.16.5

loaded via a namespace (and not attached):
[1] tools_3.1.3

Can anyone help me. I'm very new to R and its packages. I do all my work in R Studio.

Thanks in advance

 

Gareth, University of Manchester

ADD COMMENTlink modified 3.5 years ago • written 3.6 years ago by gareth.howell0

Please include the complete output of the commands you are using to install flowClust (including the commands themselves) and the output of the sessionInfo() command. You can edit your existing post.

ADD REPLYlink written 3.6 years ago by Dan Tenenbaum ♦♦ 8.2k

You error message indicates that 'MCMCpack' package is not installed properly.

ADD REPLYlink written 3.5 years ago by Jiang, Mike1.2k

Hi Mike, thanks for your response. Would you have any suggestions as to how i can go about remedying this? Gareth

ADD REPLYlink written 3.5 years ago by gareth.howell0

Run `install.packages("MCMCpack")` and make sure it is successful without errors. Then `biocLite("flowClust")`

ADD REPLYlink written 3.5 years ago by Jiang, Mike1.2k
0
gravatar for gareth.howell
3.5 years ago by
United Kingdom
gareth.howell0 wrote:

Reinstalling the MCMCpack had done the trick. Thanks for your help. 

ADD COMMENTlink written 3.5 years ago by gareth.howell0
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