i can't install metade package
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1006920318 • 0
@1006920318-23535
Last seen 3.9 years ago

when i bioconductor::install ("MetaDE"). IT'S GOING WRONG .

> BiocManager::install("MetaDE")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'MetaDE'
Installation path not writeable, unable to update packages: boot, class, foreign,
  KernSmooth, MASS, nnet, spatial
Old packages: 'ellipsis', 'glue'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
         binary source needs_compilation
ellipsis  0.3.0  0.3.1              TRUE
glue      1.4.0  1.4.1              TRUE

  Binaries will be installed
try to open URL’https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.0/ellipsis_0.3.0.zip'
Content type 'application/zip' length 44558 bytes (43 KB)
downloaded 43 KB

try to open URL’https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.0/glue_1.4.0.zip'
Content type 'application/zip' length 158875 bytes (155 KB)
downloaded 155 KB

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

The downloaded binary packages are in
    C:\Users\lenovo\AppData\Local\Temp\RtmpOuJFAj\downloaded_packages
Warning messages:
1: package ‘MetaDE’ is not available (for R version 4.0.0) 
2: In file.copy(savedcopy, lib, recursive = TRUE) :
 Copy C:\Users\lenovo\Documents\R\win-library\4.0\00LOCK\ellipsis\libs\x64\ellipsis.dll to C:\Users\lenovo\Documents\ libs\x64\ellipsis.dll with Permission denied
3: In file.copy(savedcopy, lib, recursive = TRUE) : 
Copy C:\Users\ Documents\R\win-library\4.0\00LOCK\glue\libs\x64\ glgles.dll to C:\Users\ Documents\ libs\x64\ glgles.dll: Permission denied

 >
software error • 1.6k views
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Kevin Blighe ★ 3.9k
@kevin
Last seen 1 day ago
Republic of Ireland

Hey,

MetaDE is not a Bioconductor package and, in fact, it is not even anymore in the CRAN repository - it was removed from CRAN in January, 2018: https://cran.r-project.org/web/packages/MetaDE/index.html

It seems that some now recommend metap (CRAN). My own personal recommendations are:

  • GenRank (Bioconductor)
  • RankProd (Bioconductor)

If you must use MetaDE, then you could try to install the last known version by downloading from here, and then using, for example:

install.packages('MetaDE_1.0.5.tar.gz', repos = NULL, type = 'source')

The Github repo for the package can also still be installed:

devtools::install_github('metaOmics/MetaDE')

--------------------

Kevin

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thank y very much ,i'l try it tomorrow

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can i install this package in r4.0.0 or i have to install it in earlier r , such as r 3.6.1

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Due to the fact that the MetaDE package is no longer being maintained and is not part of any central repository (CRAN or Bioconductor), there is no guarantee in which version of R it will function. If anything, it will be less likely to function on newer versions of R. I tried it today on R 3.6.3 and it worked AOK.

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ok i'll try on r 3.6.3

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do i have to delete r 4.0.0?

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Please try on r 4.0.0 if that is what you are using. However, please be aware that the package is no longer being maintained. It's functionality may not be what you expect.

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it worked 。thank y very much

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how can i view the source code for MetaD. I want to change DL algorithm, but in other packages it is not a public function

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