failling to install biomaRt
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Entering edit mode
sp59292003 • 0
@sp59292003-22742
Last seen 2.3 years ago

Sorry, I'm a new user of R language I am fail to install biomaRt in R or Rstudio running as administrator and the warning messages are below. Please can someone help me, greatly appreciated!

1: In file.copy(savedcopy, lib, recursive = TRUE) : 
 problem copying C:\Users\user\Documents\R\win-library\3.6\BiocParallel\libs\x64\BiocParallel.dll: Permission denied
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\bit\libs\x64\bit.dll to C:\Users\user\Documents\R\win-library\3.6\bit\libs\x64\bit.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\DelayedArray\libs\x64\DelayedArray.dll to C:\Users\user\Documents\R\win-library\3.6\DelayedArray\libs\x64\DelayedArray.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\digest\libs\x64\digest.dll to C:\Users\user\Documents\R\win-library\3.6\digest\libs\x64\digest.dll: Permission denied
5: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\IRanges\libs\x64\IRanges.dll to C:\Users\user\Documents\R\win-library\3.6\IRanges\libs\x64\IRanges.dll: Permission denied
6: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\RCurl\libs\x64\RCurl.dll to C:\Users\user\Documents\R\win-library\3.6\RCurl\libs\x64\RCurl.dll: Permission denied
7: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\user\Documents\R\win-library\3.6\rlang\libs\x64\rlang.dll: Permission denied
8: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\RSQLite\libs\x64\RSQLite.dll to C:\Users\user\Documents\R\win-library\3.6\RSQLite\libs\x64\RSQLite.dll: Permission denied
9: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\S4Vectors\libs\x64\S4Vectors.dll to C:\Users\user\Documents\R\win-library\3.6\S4Vectors\libs\x64\S4Vectors.dll: Permission denied
10: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\stringi\libs\icudt61l.dat to C:\Users\user\Documents\R\win-library\3.6\stringi\libs\icudt61l.dat: Invalid argument
11: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\stringi\libs\x64\stringi.dll to C:\Users\user\Documents\R\win-library\3.6\stringi\libs\x64\stringi.dll: Permission denied
12: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\testthat\libs\x64\testthat.dll to C:\Users\user\Documents\R\win-library\3.6\testthat\libs\x64\testthat.dll: Permission denied
13: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\vctrs\libs\x64\vctrs.dll to C:\Users\user\Documents\R\win-library\3.6\vctrs\libs\x64\vctrs.dll: Permission denied
14: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\XML\libs\x64\XML.dll to C:\Users\user\Documents\R\win-library\3.6\XML\libs\x64\XML.dll: Permission denied
15: In install.packages(update[instlib == l, "Package"], l,  ... :
  installation of package ‘blob’ had non-zero exit status
16: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.1\library\00LOCK\foreign\libs\x64\foreign.dll to C:\Program Files\R\R-3.6.1\library\foreign\libs\x64\foreign.dll: Permission denied
17: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.1\library\00LOCK\Matrix\libs\x64\Matrix.dll to C:\Program Files\R\R-3.6.1\library\Matrix\libs\x64\Matrix.dll: Permission denied
18: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Program Files\R\R-3.6.1\library\00LOCK\survival\libs\x64\survival.dll to C:\Program Files\R\R-3.6.1\library\survival\libs\x64\survival.dll: Permission denied
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Entering edit mode

Sorry, below is the whole message

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install("biomaRt")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'biomaRt'
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/biomaRt_2.42.0.zip'
Content type 'application/zip' length 632189 bytes (617 KB)
downloaded 617 KB

package ‘biomaRt’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\RtmpQDdp2T\downloaded_packages
Installation path not writeable, unable to update packages: foreign, Matrix, survival
Old packages: 'BiocParallel', 'bit', 'blob', 'DelayedArray', 'digest', 'IRanges', 'RCurl', 'rlang',
  'RSQLite', 'S4Vectors', 'stringi', 'testthat', 'vctrs', 'XML', 'xts', 'zoo'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
           binary   source needs_compilation
blob        1.2.0    1.2.1             FALSE
RCurl   1.95-4.13 1.98-1.1              TRUE
stringi     1.4.4    1.4.5              TRUE
XML     3.98-1.20 3.99-0.3              TRUE
xts        0.11-2   0.12-0              TRUE
zoo         1.8-6    1.8-7              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.10/bioc/bin/windows/contrib/3.6/BiocParallel_1.20.1.zip'
Content type 'application/zip' length 1672038 bytes (1.6 MB)
downloaded 1.6 MB

...    
trying URL 'https://cran.rstudio.com/src/contrib/blob_1.2.1.tar.gz'
Content type 'application/x-gzip' length 10099 bytes
downloaded 10099 bytes

* installing *source* package 'blob' ...
** package 'blob' successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'vctrs' 0.2.0 is being loaded, but >= 0.2.1 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'blob'
* removing 'C:/Users/user/Documents/R/win-library/3.6/blob'
* restoring previous 'C:/Users/user/Documents/R/win-library/3.6/blob'
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@james-w-macdonald-5106
Last seen 21 minutes ago
United States

Thanks for re-posting. Do note that you could have also simply fixed your original post, which is probably the better way to go. Also, simply highlighting your code and clicking on the box that has 101010 in it will convert the text to code, which is much easier to read.

Anyway, did you notice this part?

namespace 'vctrs' 0.2.0 is being loaded, but >= 0.2.1 is required 

Which seems pretty clear? A simple BiocManager::install("vctrs") in a new R session is likely to fix that.

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Thank you for your reply!

I tried the command to install vctrs, but the situation as mentioned in the original question remains > < Still can't install biomaRt on my windows computer.

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0
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You'll need to be more precise. Does

library(vctrs)

work, and does packageVersion('vctrs') return 0.2.1 ? The previous report involved the package 'blob'. Does

library(blob)

work, or if not does

BiocManager::install("blob")

work? If not, how does it fail? If it does work, then what is the error message you now see when trying to install biomaRt? Can you trouble shoot that error message on your end some more, e.g., if it says that 'failed to load namespace FOO', can you install FOO?

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I've done every command and one of the message below >< Sorry, I am too dumb to find out what to do next...

I've done all the command you mentioned and all came back with (can't remove prior installation of package "bala bala") and warnings show "Permission denied"

> BiocManager::install("blob")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'blob'
also installing the dependency ‘vctrs’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/vctrs_0.2.1.zip'
Content type 'application/zip' length 829973 bytes (810 KB)
downloaded 810 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/blob_1.2.1.zip'
Content type 'application/zip' length 47769 bytes (46 KB)
downloaded 46 KB

package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘blob’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\RtmpiIEiSp\downloaded_packages
Old packages: 'BiocParallel', 'bit', 'DelayedArray', 'digest', 'IRanges', 'RCurl',
  'rlang', 'RSQLite', 'S4Vectors', 'stringi', 'testthat', 'XML', 'zoo', 'foreign',
  'Matrix', 'survival'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
        binary source needs_compilation
stringi  1.4.4  1.4.5              TRUE
zoo      1.8-6  1.8-7              TRUE

  Binaries will be installed
Warning: packages ‘BiocParallel’, ‘DelayedArray’, ‘IRanges’, ‘S4Vectors’ are in use and will not be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/bit_1.1-15.1.zip'
Content type 'application/zip' length 253208 bytes (247 KB)
downloaded 247 KB

package ‘bit’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘bit’
Warning: restored ‘bit’
package ‘digest’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘digest’
Warning: restored ‘digest’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/Matrix_1.2-18.zip'
Content type 'application/zip' length 4524025 bytes (4.3 MB)
downloaded 4.3 MB

package ‘foreign’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘foreign’
Warning: restored ‘foreign’
package ‘Matrix’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Matrix’
Warning: restored ‘Matrix’

The downloaded binary packages are in
    C:\Users\user\AppData\Local\Temp\RtmpiIEiSp\downloaded_packages
There were 11 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\bit\libs\x64\bit.dll to C:\Users\user\Documents\R\win-library\3.6\bit\libs\x64\bit.dll: Permission denied
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\digest\libs\x64\digest.dll to C:\Users\user\Documents\R\win-library\3.6\digest\libs\x64\digest.dll: Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\RCurl\libs\x64\RCurl.dll to C:\Users\user\Documents\R\win-library\3.6\RCurl\libs\x64\RCurl.dll: Permission denied
4: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\rlang\libs\x64\rlang.dll to C:\Users\user\Documents\R\win-library\3.6\rlang\libs\x64\rlang.dll: Permission denied
5: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\stringi\libs\icudt61l.dat to C:\Users\user\Documents\R\win-library\3.6\stringi\libs\icudt61l.dat: Invalid argument
6: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\stringi\libs\x64\stringi.dll to C:\Users\user\Documents\R\win-library\3.6\stringi\libs\x64\stringi.dll: Permission denied
7: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\testthat\libs\x64\testthat.dll to C:\Users\user\Documents\R\win-library\3.6\testthat\libs\x64\testthat.dll: Permission denied
8: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\user\Documents\R\win-library\3.6\00LOCK\XML\libs\x64\XML.dll to C:\Users\user\Documents\R\win-library\3.6\XML\libs\x64\XML.dll: Permission denied
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Entering edit mode

So it looks like the original error

** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'vctrs' 0.2.0 is being loaded, but >= 0.2.1 is required

has been solved? The remaining WARNINGS are present because you installed some packages as administrator, but you are now trying to update them as a regular user. The correct solution is to start again (remove your current R installation and libraries) and install all packages as a regular user.

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Entering edit mode

It works!!! I removed the old R and Rstudio then installed again. Thank you so much!!!!

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thanks for your advice, it helped just restarting gui with administrator rights. not very safe though, i suppose...

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