Problem installing packages including flowWorkspace
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Entering edit mode
Alice ▴ 10
@30e2b8a7
Last seen 6 weeks ago
United States

Hi, I have issues installing several packages including flowWorkspace. Could you help me with this issue?


> BiocManager::install("flowWorkspace")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.12 (BiocManager 1.30.16), R 4.0.4 (2021-02-15)
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.0.4/library
  packages:
    boot, class, cluster, KernSmooth, lattice, MASS, Matrix, mgcv, nnet, spatial, survival
Old packages: 'dplyr', 'ellipsis', 'ps', 'rlang', 'stringi', 'testthat'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
        binary source needs_compilation
dplyr    1.0.6  1.0.7              TRUE
stringi  1.5.3  1.6.2              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/dplyr_1.0.6.zip'
Content type 'application/zip' length 1339313 bytes (1.3 MB)
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/ellipsis_0.3.2.zip'
Content type 'application/zip' length 49135 bytes (47 KB)
downloaded 47 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/ps_1.6.0.zip'
Content type 'application/zip' length 776205 bytes (758 KB)
downloaded 758 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rlang_0.4.11.zip'
Content type 'application/zip' length 1202829 bytes (1.1 MB)
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/stringi_1.5.3.zip'
Content type 'application/zip' length 15243599 bytes (14.5 MB)
downloaded 14.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/testthat_3.0.3.zip'
Content type 'application/zip' length 2502690 bytes (2.4 MB)
downloaded 2.4 MB

package ‘dplyr’ successfully unpacked and MD5 sums checked
package ‘ellipsis’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘ellipsis’
Warning: restored ‘ellipsis’
package ‘ps’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘ps’
Warning: restored ‘ps’
package ‘rlang’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘rlang’
Warning: restored ‘rlang’
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘testthat’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘testthat’
Warning: restored ‘testthat’

The downloaded binary packages are in
    C:\Users\alice\AppData\Local\Temp\Rtmpiw1grU\downloaded_packages
Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'flowWorkspace' 
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\alice\OneDrive\Documents\R\win-library\4.0\00LOCK\ellipsis\libs\x64\ellipsis.dll to C:\Users\alice\OneDrive\Documents\R\win-library\4.0\ellipsis\libs\x64\ellipsis.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\alice\OneDrive\Documents\R\win-library\4.0\00LOCK\ps\libs\x64\ps.dll to C:\Users\alice\OneDrive\Documents\R\win-library\4.0\ps\libs\x64\ps.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\alice\OneDrive\Documents\R\win-library\4.0\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\alice\OneDrive\Documents\R\win-library\4.0\rlang\libs\x64\rlang.dll: Permission denied
5: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\alice\OneDrive\Documents\R\win-library\4.0\00LOCK\testthat\libs\x64\testthat.dll to C:\Users\alice\OneDrive\Documents\R\win-library\4.0\testthat\libs\x64\testthat.dll: Permission denied

> library(flowWorkspace)
Error: package or namespace load failed for ‘flowWorkspace’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace ‘ellipsis’ 0.3.1 is already loaded, but >= 0.3.2 is required

Thank you for your help!

transcriptR • 177 views
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On quick glance, it appears you do not have write access to the library directory in order to update the packages? Was R or these packages installed under a different username/account?

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ATpoint ▴ 720
@atpoint-13662
Last seen 7 hours ago
Germany

Try starting a new R session and then load the package again. If that fails then manually install ellipsis version 0.3.2 or greater. By the way, the title of this post is unfortunate, you may want to change that to something that is relevant for the question.

namespace ‘ellipsis’ 0.3.1 is already loaded, but >= 0.3.2 is required

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