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Question: Windows 10 openCyto Install: installation path not writeable, unable to update packages: boot, Matrix, mgcv
0
gravatar for Robert Baer
12 months ago by
Robert Baer70
United States
Robert Baer70 wrote:

I get the error in the title when I try to install the openCyto package or when I do a straight forward run of biocLite() with no arguments.

In the case of openCyto I get the message at the end after an appaently successful install of openCyto.  Subsequently, "library(openCyto) fails ostensibly because it can't find flowClust()

Two questions:

1)  Is the flowClust failure secondary to the filepath issue of biocLite() for boot, Matrix, and mgv and if so, how do I fix it?

2)  What should I do to get openCyto  to work properly? 

Here is some context:

> ## try http:// if https:// URLs are not supported

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

Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help

> biocLite("openCyto")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1

  (2017-06-30).

Installing package(s) ‘openCyto’

also installing the dependency ‘flowClust’


Package which is only available in source form, and may need

  compilation of C/C++/Fortran: ‘flowClust’

  These will not be installed

trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/openCyto_1.14.0.zip'

Content type 'application/zip' length 3728048 bytes (3.6 MB)

downloaded 3.6 MB


package ‘openCyto’ successfully unpacked and MD5 sums checked


The downloaded binary packages are in

C:\Users\rbaer\AppData\Local\Temp\RtmpUlczKU\downloaded_packages

installation path not writeable, unable to update packages: boot,

  Matrix, mgcv

> library(openCyto)

Error: package or namespace load failed for ‘openCyto’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called ‘flowClust’

-------------------------

A check with biocLite()  suggests that I might be having a more general problem with install paths, but my .libPaths() seems to include a perfectly writable folder in my user folder.  Any idea how to proceed in getting openCyto installed or better-state "usable".?

 

This seems like it should have an easy solution, but I could not find one in the FAQ. My local path has

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
> biocLite()                  ## R version 3.0 or later
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1
  (2017-06-30).
installation path not writeable, unable to update packages: boot,
  Matrix, mgcv
> .libPaths()
[1] "C:/Users/rbaer/Documents/R/win-library/3.4"
[2] "C:/Program Files/R/R-3.4.1/library"        
> R.Version()
$platform
[1] "x86_64-w64-mingw32"

$arch
[1] "x86_64"

$os
[1] "mingw32"

$system
[1] "x86_64, mingw32"

$status
[1] ""

$major
[1] "3"

$minor
[1] "4.1"

$year
[1] "2017"

$month
[1] "06"

$day
[1] "30"

$`svn rev`
[1] "72865"

$language
[1] "R"

$version.string
[1] "R version 3.4.1 (2017-06-30)"

$nickname
[1] "Single Candle"

---------------------------------

Finally, sessionInfo() :

> sessionInfo()
R version 3.4.1 (2017-06-30)
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 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] flowWorkspace_3.24.4      ncdfFlow_2.22.2          
[3] BH_1.65.0-1               RcppArmadillo_0.7.960.1.2
[5] flowCore_1.42.3           BiocInstaller_1.26.1     

loaded via a namespace (and not attached):
 [1] lattice_0.20-35     pcaPP_1.9-72        colorspace_1.3-2   
 [4] stats4_3.4.1        RBGL_1.52.0         XML_3.98-1.9       
 [7] rlang_0.1.2         R.oo_1.21.0         hexbin_1.27.1      
[10] glue_1.1.1          R.utils_2.5.0       Rgraphviz_2.20.0   
[13] BiocGenerics_0.22.0 RColorBrewer_1.1-2  bindrcpp_0.2       
[16] matrixStats_0.52.2  bindr_0.1           plyr_1.8.4         
[19] robustbase_0.92-7   stringr_1.2.0       zlibbioc_1.22.0    
[22] munsell_0.4.3       gtable_0.2.0        R.methodsS3_1.7.1  
[25] mvtnorm_1.0-6       latticeExtra_0.6-28 Biobase_2.36.2     
[28] parallel_3.4.1      DEoptimR_1.0-8      Rcpp_0.12.12       
[31] KernSmooth_2.23-15  corpcor_1.6.9       scales_0.5.0       
[34] graph_1.54.0        IDPmisc_1.1.17      gridExtra_2.3      
[37] stringi_1.1.5       dplyr_0.7.3         clue_0.3-54        
[40] grid_3.4.1          tools_3.4.1         magrittr_1.5       
[43] tibble_1.3.4        cluster_2.0.6       rrcov_1.4-3        
[46] pkgconfig_2.0.1     MASS_7.3-47         flowViz_1.40.0     
[49] data.table_1.10.4   assertthat_0.2.0    R6_2.2.2           
[52] compiler_3.4.1  

 

ADD COMMENTlink modified 7 months ago by Jiang, Mike1.1k • written 12 months ago by Robert Baer70
0
gravatar for Samuel Ahuno
12 months ago by
Ghana/KNUST
Samuel Ahuno0 wrote:

Hey my friend.....

Try running R or R-studio as administrator.

Simply right-click the "R" icon on your start and run as administrator if using windows.

I hoe this helps!

Best

Sam

 

ADD COMMENTlink written 12 months ago by Samuel Ahuno0

Actually, the problem probably came about because someone ran R as Administrator. Better to always run R as a non-privileged user, correcting the previous installation by, e.g., starting over.

ADD REPLYlink written 12 months ago by Martin Morgan ♦♦ 22k
0
gravatar for Samuel Ahuno
7 months ago by
Ghana/KNUST
Samuel Ahuno0 wrote:

Hi there,

Sometimes I could be because you have multiple R programs opened for example having "R studio" and "R base" running at the same time.

Close one of these programs and lets see whether is resolved.

Best

Sam

ADD COMMENTlink written 7 months ago by Samuel Ahuno0
0
gravatar for Jiang, Mike
7 months ago by
Jiang, Mike1.1k
(Private Address)
Jiang, Mike1.1k wrote:

The error was about the failure in installing flowClust package. You were currently using Bioconductor 3.5. The issue should be resolved if you upgrade to Bioconductor 3.6 (the latest release, and you may need to upgrade your R to 3.4.3)

 

ADD COMMENTlink written 7 months ago by Jiang, Mike1.1k
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