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RahmanTeam / DECoN

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Failed installation #18

Open alejandroriglesias opened 4 years ago

alejandroriglesias commented 4 years ago

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

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:

'/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

The command failed with output:

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.

flapa86 commented 3 years ago

I've a similar error....did you find the solution? I've R version 3.6.0

zgtman commented 3 years ago

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.

seon22break commented 3 years ago

I've a similar error....did you find the solution? I've R version 3.6.0

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.

zgtman commented 3 years ago

Yes I did - use Exome Depth for CNV calling - works perfectly fine.

ClaraffD commented 3 years ago

I've a similar error....did you find the solution? I've R version 3.6.0

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.

Hi, have you created your Docker image? Running out of options to successfully use DECoN here.. thank you!

seon22break commented 3 years ago

I've a similar error....did you find the solution? I've R version 3.6.0

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.

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

ClaraffD commented 3 years ago

I've a similar error....did you find the solution? I've R version 3.6.0

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.

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

worker000000 commented 3 years ago

Yes I did - use Exome Depth for CNV calling - works perfectly fine.

do you kown which column of exomedepth stands for copy number, thanks a lot and have you ever met this https://github.com/vplagnol/ExomeDepth/issues/44

worker000000 commented 3 years ago

@ClaraffD i once download one, not writen by me, but it needs to enter the docker, can not concatate argument directly, not that convenient

#################################################################

Dockerfile # # Version: 0.1

Software: DECoN V1.0.2

Description: DECoN Detection of Exon Copy Number variants

Website: http://www.thetgmi.org/tgmi-news/detecting-tricky-gene-mutations/

Tags: None, for the moment

Base Image: r-base:3.1.2

################################################################# From r-base:3.1.2 ENTRYPOINT ["/bin/bash"]

Adding user decon

RUN useradd -ms /bin/bash decon

Adding Certificates for wget tu download from git

RUN apt-get update && \ apt-get install -y --no-install-recommends \ ca-certificates \ && rm -rf /var/lib/apt/lists/*

Running Container as decon and install decon from git

USER decon WORKDIR /home/decon/ RUN wget https://github.com/RahmanTeam/DECoN/archive/v1.0.2.tar.gz RUN tar -xzvf v1.0.2.tar.gz Run rm v1.0.2.tar.gz WORKDIR /home/decon/DECoN-1.0.2/Linux/

Starting setup

RUN mkdir /home/decon/DECoN-1.0.2/Linux/packrat/src/VGAM/ RUN wget https://cran.r-project.org/src/contrib/Archive/VGAM/VGAM_0.9-8.tar.gz -O /home/decon/DECoN-1.0.2/Linux/packrat/src/VGAM/VGAM_0.9-8.tar.gz RUN ./setup.sh