Windows 10 openCyto Install: installation path not writeable, unable to update packages: boot, Matrix, mgcv
3
0
Entering edit mode
Robert Baer ▴ 70
@robert-baer-4660
Last seen 15 months ago
United States

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  

 

bioclite openCyto package installation • 1.6k views
ADD COMMENT
0
Entering edit mode
@samuel-ahuno-14031
Last seen 3.0 years ago
Ghana/KNUST

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode
@samuel-ahuno-14031
Last seen 3.0 years ago
Ghana/KNUST

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 COMMENT
0
Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 9 months ago
(Private Address)

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 COMMENT

Login before adding your answer.

Traffic: 249 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6