Cannot install the FlowWorkSpaceData package
1
1
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@afgirigorie-23034
Last seen 4.2 years ago

Hi everyone,

I'm a real newbie with Bioconductor and can manage with R. Right now I'm trying out different flow cytometry packages to see which are the ones I will be using for the research that is going on in the lab I'm working in.

Now while I was installing some data that comes along with the FlowWorkSpace package to familiarize myself with it but when trying to install I get this message:

> BiocManager::install("flowWorkspaceData")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'flowWorkspaceData'
installing the source package ‘flowWorkspaceData’

trying URL 'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/flowWorkspaceData_2.22.0.tar.gz'
Content type 'application/x-gzip' length 36957917 bytes (35.2 MB)
downloaded 35.2 MB

'\\amc.intra\users\A\afgirigorie\home'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
* installing *source* package 'flowWorkspaceData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in findpack(package, lib.loc) : 
  there is no package called 'flowWorkspaceData'
Calls: <Anonymous> -> findpack
Execution halted
ERROR: lazy loading failed for package 'flowWorkspaceData'
* removing '\\amc.intra/users/A/afgirigorie/home/R/win-library/3.6/flowWorkspaceData'

The downloaded source packages are in
    ‘C:\Users\afgirigorie\AppData\Local\Temp\RtmpqCRVlZ\downloaded_packages’
Installation path not writeable, unable to update packages: lattice
Old packages: 'nnet', 'rlang'
Update all/some/none? [a/s/n]: 
n
Warning message:
In install.packages(...) :
  installation of package ‘flowWorkspaceData’ had non-zero exit status.

This is my session info:

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252    LC_MONETARY=Dutch_Netherlands.1252
[4] LC_NUMERIC=C                       LC_TIME=Dutch_Netherlands.1252    

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.3      tools_3.6.3        

Can anyone help me solve this problem?

Thank you!

software error • 644 views
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@martin-morgan-1513
Last seen 20 days ago
United States

\\amc.intra/users is a 'network path', which R does not like. You can search for 'map network drive' to associate a letter, e.g., W: with this path, and then arrange for R to use that path; this StackOverflow answer https://stackoverflow.com/a/31707983/547331 provides some useful hints.

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Alright! I will go and try it. Thank you for the help.

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It seems that is was a lot of trouble for nothing. I got this after I changed the path:

> install.packages("flowWorkspaceData")
Warning in install.packages :
  'lib = "C:/Program Files/R/R-3.6.3/library"' is not writable
Warning in install.packages :
  package ‘flowWorkspaceData’ is not available (for R version 3.6.3)
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flowWorkspaceData is a Bioconductor package, and so should be installed with BiocManager::install("flowWorkspaceData").

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That is what I tried at first and that still doesn't work, and changing the path also doesn't help. I'm still trying to solve the problem (I'm probably missing something simple to fix it).

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Can you now report what the error is? Previously it was "UNC paths are not supported" but now you do not have UNC paths, so the error must be different...

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Hi,

It took some time, but it seems that the IT department seems to have rolled out an update that is affecting a lot of computers in the institute. So I need to be patient and wait. But thanks for thinking along with me to try and fix this problem.

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