SNPHYLO install problem for linux (CentOS 6)

[moko-moko]

Hello,

I have install problems. Perhaps, these are R repository errors. My command and Error massages are below :

$ bash setup.sh Version: 20141127

START TO SET UP FOR SNPHYLO!!!

The detected path of R is /usr/bin/R. Is it correct? [Y/n] y The detected path of python is /home/minako/anaconda3/bin/python. Is it correct? [Y/n] y muscle is not found. Is the program already installed? [y/N] y Please enter the path of muscle program (ex: /home/foo/bin/muscle): /home/minako/snphylo/bin/muscle

dnaml is not found. Is the program already installed? [y/N] y Please enter the path of dnaml program (ex: /home/foo/bin/dnaml): /home/minako/snphylo/phylip/exe/dnaml At least one R package (gdsfmt, SNPRelate, getopt or phangorn) to run this pipeline is not found. Are the packages already installed? [y/N] n Do you want to install the packages by this script? [y/N] y

~ The downloaded source packages are in '/tmp/RtmpMuNZRV/downloaded_packages' Old packages: 'getopt'

Fail to install the packages. :(

You can download the packages at http://cran.r-project.org/web/packages/getopt/index.html, http://cran.r-project.org/src/contrib/Archive/gdsfmt/ and http://cran.r-project.org/src/contrib/Archive/SNPRelate/. Please, download and install the packages and restart this script.

//

Please repair the scripts.

Thank you.

[moko-moko]

I installed R packages (phangorn, gdsfmt, SNPRelate and getopt) manually. successfully installed.

[stly1996]

But after installed R packages (phangorn, gdsfmt, SNPRelate and getopt) manually, it will still apper "At least one R package (gdsfmt, SNPRelate, getopt or phangorn) to run this pipeline is not found. Are the packages already installed? [y/N] "

If reply y, it will apper "Please enter the directory for R packages (ex: /home/foo/r_packages): " How can I find the path which it need?

[guandailu]

how to fix it?

[stly1996]

I don't know whether you still need it or not. I fix it by install the newest R to solve it.

[Tman3]

Does SNPhylo needs phangorn to run? I have trouble to install it due to issues with igraph.

Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/abc/R/x86_64-pc-linux-gnu-library/3.4/igraph/libs/igraph.so': libgfortran.so.4: cannot open shared object file: No such file or directory

Have updated the gfortran on the system, but still not able to install phangorn. Any suggestion is appreciated.

[Tman3]

[Solved] Used g++-7 instead and used soft link to connect g++-7 with libgfortran.so.4 to solve the problem.

[criskzimpel]

Hi, I was having the very same problem. I was able to fix it just moving the folder with the packages (that for me was in "/private/var/folders/5c/f6_bp_fn7gdg2ymt8x3dw8j80000gn/T/Rtmpv3IIBN/downloaded_packages" ) to /Library/Frameworks/R.framework/Versions/3.5/Resources.

Then I ran snphylo:

"bash setup.sh

START TO SET UP FOR SNPHYLO!!!

The detected path of R is /usr/local/bin/R. Is it correct? [Y/n] y The detected path of python is /usr/bin/python. Is it correct? [Y/n] y muscle is not found. Is the program already installed? [y/N] y Please enter the path of muscle program (ex: /home/foo/bin/muscle): //PATH/to/muscle

dnaml is not found. Is the program already installed? [y/N] y Please enter the path of dnaml program (ex: /home/foo/bin/dnaml): /PATH/to/dnaml

SNPHYLO is successfully installed!!!"

[Yixiangzhang1996]

I installed R packages (phangorn, gdsfmt, SNPRelate and getopt) manually.But it didnt work. I have tried it all day.

`(base) [zyx@node02 SNPhylo]$ bash setup.sh Version: 20141127

START TO SET UP FOR SNPHYLO!!!

The detected path of R is /cluster/anaconda2/bin/R. Is it correct? [Y/n] y The detected path of python is /home1/zyx/miniconda3/bin/python. Is it correct? [Y/n] y The detected path of muscle is /home1/zyx/miniconda3/bin/muscle. Is it correct? [Y/n] y The detected path of dnaml is /cluster/anaconda2/bin/dnaml. Is it correct? [Y/n] y

At least one R package (gdsfmt, SNPRelate, getopt or phangorn) to run this pipeline is not found. Are the packages already installed? [y/N] Do you want to install the packages by this script? [y/N] y Warning: unable to access index for repository http://cran.r-project.org/src/contrib: cannot open URL 'http://cran.r-project.org/src/contrib/PACKAGES' Warning message: package ‘getopt’ is not available (for R version 3.3.1) Warning: unable to access index for repository http://cran.r-project.org/src/contrib: cannot open URL 'http://cran.r-project.org/src/contrib/PACKAGES' Warning message: package ‘phangorn’ is not available (for R version 3.3.1) Error in file(filename, "r", encoding = encoding) : cannot open the connection Calls: source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : unable to resolve 'bioconductor.org' Execution halted

Fail to install the packages. :(

You can download the packages at http://cran.r-project.org/web/packages/getopt/index.html, http://cran.r-project.org/src/contrib/Archive/gdsfmt/ and http://cran.r-project.org/src/contrib/Archive/SNPRelate/. Please, download and install the packages and restart this script. `

[mah460]

Hi, I have the same issue but a bit more complicated. I am using Ubuntu for installing the SNPphylo. I have installed the programs and files according to the instruction. However, the command "bash setup.sh" is not working at all. It gives the error: bash: setup.sh: No such file or directory So, I don't know if the problem is with my terminal or the packages/ programs?! I followed all instructions in: http://chibba.pgml.uga.edu/snphylo/install_on_linux.html However, didnt install the R packages manually? I don't know how to do it in ubuntu! I thought the packages will be installed after setup but have issue to reach that stage.

Please help. Thanks, Mah