PhylotaR Cluster error: blastn failed to run about phylotar HOT 8 CLOSED

Hi!

This looks similar to an error I fixed. Try installing the latest version from GitHub with the library remotes:

library(remotes)
install_github('ropensci/phylotar')

from phylotar.

I've tried installing phylotaR with the code suggested, but I get the following error:

Error: Failed to install 'phylotaR' from GitHub:
(converted from warning) package ‘restez’ is not available (for R version 3.4.4)

Has the package been removed from the CRAN repository or do I simply need to use another R version?

from phylotar.

Ah whoops.... restez got removed from CRAN due to a key dep being archived. Try:

library(remotes)
# install restez dep
install_github("hannesmuehleisen/MonetDBLite-R")
# install restez
install_github("ropensci/restez")
# install phylotaR
install_github('ropensci/phylotar')

from phylotar.

I cannot seem to install MonetDBLite. I get the following error:

Error: Failed to install 'MonetDBLite' from GitHub:
(converted from warning) running command '"C:/PROGRA1/R/R-341.1/bin/x64/R" CMD INSTALL -l "C:\Users\maari\OneDrive\Documentos\R\win-library\3.4" "C:/Users/maari/AppData/Local/Temp/Rtmpqm9Xz8/file20b45323f55/MonetDBLite_0.6.1.tar.gz"' had status 1
In addition: Warning message:
In missing_devel_warning(pkgdir) :
Package MonetDBLite has compiled code, but no suitable compiler(s) were found. Installation will likely fail.
Install Rtools (https://cran.r-project.org/bin/windows/Rtools/).Then use the pkgbuild package, or make sure that Rtools in the PATH.

Any idea how I can solve this?

from phylotar.

Hi!

The error message is asking you to install "Rtools". This is an additional software, specific to Windows, that some R packages require. (It is also required for buidling and developing packages.)

Go to this link (https://cran.r-project.org/bin/windows/Rtools/), install Rtools and then try to reinstall MonetDBLite.

Thanks!

from phylotar.

Hi,

I've managed to make it work, turns out the problem was in the path to Rtools.

But now, the setup doesn't run smoothly. I've used the same code:

library(phylotaR)
wd <- 'C:/Users/maari/Desktop/1. LIFELINE/phylotaR/Rotaria'
ncbi_dr <- 'C:/Program Files/NCBI/blast-2.9.0+/bin'
txid <- 231623
setup(wd = wd, txid = txid, ncbi_dr = ncbi_dr, v = T)

And I get the error:

phylotaR: Implementation of PhyLoTa in R [v1.2.0]

Checking for valid NCBI BLAST+ Tools ...
Found: [C:/Program Files/NCBI/blast-2.9.0+/bin/makeblastdb]
Found: [C:/Program Files/NCBI/blast-2.9.0+/bin/blastn]
. . Running makeblastdb
Error: makeblastdb failed to run. Check BLAST log files.

I've checked and the blast folder has no log, only a file called testdbfl.

from phylotar.

For info, we're looking for a new maintainer / a new maintainer team for this package, see #57 and feel free to volunteer, we'd be happy to help.

from phylotar.

This is similar to #39, it should work in the latest version. If not, please file a new issue.

from phylotar.