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vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
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install Error #51

Closed user-tq closed 1 year ago

user-tq commented 1 year ago

i try to install DEcON,but it cant install ExomeDepth

Retrieving 'https://cran.ma.imperial.ac.uk/src/contrib/Archive/ExomeDepth/ExomeDepth_1.1.15.tar.gz' ...
Warning: failed to find source for 'ExomeDepth 1.1.15' in package repositories
Warning: failed to retrieve 'https://cran.ma.imperial.ac.uk/src/contrib/Archive/ExomeDepth/ExomeDepth_1.1.15.tar.gz' [error code 22]
Error: failed to retrieve package 'ExomeDepth@1.1.15'
In addition: There were 11 warnings (use warnings() to see them)
Traceback (most recent calls last):

try to rearch ExomeDepth on cran ,I get that image https://cran.r-project.org/web/packages/ExomeDepth/index.html

vplagnol commented 1 year ago

Thanks and yes I am aware.

CRAN is objecting to the fact that I incldued some GSL library code (all open source) into my package instead of having it as a dependency. I find it absolutely silly- GSL is large and it was easier for me to copy chunks of code, with all the proper attributions in the code base. I'll try to sort it out with CRAN, so apologies about this.

On Fri, Oct 14, 2022 at 10:11 AM user-tq @.***> wrote:

i try to install DEcON,but it cant install ExomeDepth

Retrieving 'https://cran.ma.imperial.ac.uk/src/contrib/Archive/ExomeDepth/ExomeDepth_1.1.15.tar.gz' ... Warning: failed to find source for 'ExomeDepth 1.1.15' in package repositories Warning: failed to retrieve 'https://cran.ma.imperial.ac.uk/src/contrib/Archive/ExomeDepth/ExomeDepth_1.1.15.tar.gz' [error code 22] Error: failed to retrieve package @.***' In addition: There were 11 warnings (use warnings() to see them) Traceback (most recent calls last):

try to rearch ExomeDepth on cran ,I get that [image: image] https://user-images.githubusercontent.com/72878144/195807696-072894c8-50e1-4659-8e52-d91f479e87e0.png https://cran.r-project.org/web/packages/ExomeDepth/index.html

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vplagnol commented 1 year ago

OK package back on CRAN now.

abernar-85 commented 1 year ago

I am still having same issue when installing DECoN:

Retrieving 'https://cran.ma.imperial.ac.uk/src/contrib/Archive/ExomeDepth/ExomeDepth_1.1.15.tar.gz' ... Warning: failed to find source for 'ExomeDepth 1.1.15' in package repositories Warning: failed to retrieve 'https://cran.ma.imperial.ac.uk/src/contrib/Archive/ExomeDepth/ExomeDepth_1.1.15.tar.gz' [error code 22] Error: failed to retrieve package 'ExomeDepth@1.1.15' In addition: There were 11 warnings (use warnings() to see them)

vplagnol commented 1 year ago

Yes the version of ExomeDepth on CRAN is now 1.1.16. Someone should tell DECon to look for a more recent ExomeDepth, I suppose something is hardcoded in the DECon code?