Failed installation #18
Comments
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I've a similar error....did you find the solution? |
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Absolutely agree. I try to install this tools with no success. I do not understand why developers do not put all necessary packages under the packrat directory. Still with some error. I think this project is dead. I would everybody recommend rather ExomeDepth. Thank you. |
The R version is very important and in a project like this, where they are not updating the code, I would recommend you to install the R 3.1.2 version. I am creating a Docker image with DeCoN installed. As soon as I have it, I will post it. |
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Yes I did - use Exome Depth for CNV calling - works perfectly fine. |
Hi, have you created your Docker image? Running out of options to successfully use DECoN here.. thank you! |
Yes , I have a docker image with DeCoN. Works correctly |
Would it be possible for you to link it please? Thank you for your help |
do you kown which column of exomedepth stands for copy number, thanks a lot |
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@ClaraffD ################################################################# Dockerfile # # Version: 0.1Software: DECoN V1.0.2Description: DECoN Detection of Exon Copy Number variantsWebsite: http://www.thetgmi.org/tgmi-news/detecting-tricky-gene-mutations/Tags: None, for the momentBase Image: r-base:3.1.2################################################################# Adding user deconRUN useradd -ms /bin/bash decon Adding Certificates for wget tu download from gitRUN apt-get update && Running Container as decon and install decon from gitUSER decon Starting setupRUN mkdir /home/decon/DECoN-1.0.2/Linux/packrat/src/VGAM/ |
Hello,
I am trying to install DECoN on my Mac (macOS Catalina 10.15.2). I already have gcc (installed with homebrew) and gfortran seems to be included in the gcc installation. I then try to run the setup.sh, and lots of connection errors start to appear:
_* installing source package ‘packrat’ ...
** package ‘packrat’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/bioc/bin/macosx/el-capitan/contrib/3.5:
no fue posible abrir la URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/el-capitan/contrib/3.5:
no fue posible abrir la URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/experiment/bin/macosx/el-capitan/contrib/3.5:
no fue posible abrir la URL 'http://bioconductor.org/packages/3.0/data/experiment/bin/macosx/el-capitan/contrib/3.5/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/extra/bin/macosx/el-capitan/contrib/3.5:
no fue posible abrir la URL 'http://bioconductor.org/packages/3.0/extra/bin/macosx/el-capitan/contrib/3.5/PACKAGES'_
I don't know if these warnings are important. Anyway, the program continues to execute and then jumps to the next error, which is the installation of BiocGenerics. I manually downloaded the tar.gz and skipped the error, but then another appeared.
_Installing Rcpp (0.11.6) ...
[1]
"Command failed (1)\n\nFailed to run system command:\n\n\t'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL '/private/var/folders/3q/skwv9bz16r3gc91k9ycdzq6h0000gn/T/RtmpGpOjnz/Rcpp' --library='/Users/alex/Desktop/R/Software/DECoN-master/Linux/packrat/lib/x86_64-apple-darwin15.6.0/3.5.1' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing source package 'Rcpp' ...\n** package 'Rcpp' successfully unpacked and MD5 sums checked\n** libs\nclang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -Wall -g -O2 -c Date.cpp -o Date.o\nIn file included from Date.cpp:31:\nIn file included from ../inst/include/Rcpp.h:73:\n../inst/include/Rcpp/Rmath.h:222:55: error: no member named 'Rf_pythag' in the global namespace; did you mean 'pythag'?\n inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }\n ^~~~~~~~~~~\n pythag\n../inst/include/Rcpp/Rmath.h:222:19: note: 'pythag' declared here\n inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }\n ^\n1 error generated.\nmake: *** [Date.o] Error 1\nERROR: compilation failed for package 'Rcpp'\n* removing '/Users/alex/Desktop/R/Software/DECoN-master/Linux/packrat/lib/x86_64-apple-darwin15.6.0/3.5.1/Rcpp'"
Error: Command failed (1)
Failed to run system command:
The command failed with output:
** package 'Rcpp' successfully unpacked and MD5 sums checked
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fPIC -Wall -g -O2 -c Date.cpp -o Date.o
In file included from Date.cpp:31:
In file included from ../inst/include/Rcpp.h:73:
../inst/include/Rcpp/Rmath.h:222:55: error: no member named 'Rf_pythag' in the global namespace; did you mean 'pythag'?
inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }
Además: Warning message:
In packrat::restore() :
The most recent snapshot was generated using R version 3.1.2_
I am now stuck here and cannot find a solution browsing on the internet. Anyone has any ideas? I would very much like to be able to use DECoN.
Thanks in advance.
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