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Question: Windows 10 openCyto Install: installation path not writeable, unable to update packages: boot, Matrix, mgcv
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gravatar for Robert Baer
7 weeks 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 weeks ago by ekwame0010 • written 7 weeks ago by Robert Baer70
0
gravatar for ekwame001
7 weeks ago by
ekwame0010
ekwame0010 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 7 weeks ago by ekwame0010

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 7 weeks ago by Martin Morgan ♦♦ 20k
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