ropensci / beastier Goto Github PK
View Code? Open in Web Editor NEWR package to run BEAST2
Home Page: https://docs.ropensci.org/beastier
License: GNU General Public License v3.0
R package to run BEAST2
Home Page: https://docs.ropensci.org/beastier
License: GNU General Public License v3.0
Feedback from Brian Ripley:
See https://cran.r-project.org/web/checks/check_results_beastier.html .
Your test seems wrong-headed: nothing mandates paths should start at /home on Unix: macOS uses /Users, my dept uses /homes for roving home directories and /users is quite common. And installing into ~/.local/share would be a violation of the CRAN policy ....
Please correct ASAP once all the results are in and before Jun 6 to safely retain the package on CRAN.
He is (of course) right!
Crashes now under AppVeyor.
Great resource! Do you have plans for a function to import tip dates?
Thank you!
Need it for mcbette
Feedback bjoelle:
create_posterior: it's unclear what this function is meant to be used for, as it's not exported or called from anywhere else in the package
From Martina Schmirl:
please omit the redundant "from R" in the title.
please omit double spaces in the description (e.g. "'BEAST2' from").
Please always write package names, software names and API names in single quotes (e.g. 'BEAST2', 'R') in the title and the description field.
The LICENSE file is only needed if you have additional restrictions to the GPL-3 which you have not? In that case omit the file and its reference in the DESCRIPTION file.
Please provide small executable examples in all your exported functions' Rd files to illustrate the use of the exported function but also enable automatic testing.
Please fix and resubmit.
Redirected from this Issue to here, as beastier
causes the unnecessarily verbose output on Windows.
Error: file.exists(output_log_filename) is not TRUE
In addition: Warning messages:
1: In file.rename(from = from, to = output_log_filename) :
cannot rename file 'test_output_0.log' to '/tmp/RtmpCkIwGP/file1ef65a706c8.log', reason 'Invalid cross-device link'
2: In file.rename(from = from, to = to) :
* checking examples ... ERROR
Running examples in ‘beastier-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_default_log_filename
> ### Title: Create the default '.log' filename as will be created by BEAST
> ### Aliases: create_default_log_filename
>
> ### ** Examples
>
> library(testthat)
>
> input_filename <- get_beastier_path("2_4.xml")
> log_filename <- create_default_log_filename(input_filename)
Error in check_beast2_path(beast2_path) :
'beast2_path' must be the name of an existing file. File '/home/hornik/.local/share/beast/lib/beast.jar' not found
Calls: create_default_log_filename -> check_beast2_path
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
Clear: there is no BEAST2 installed on the CRAN CI, run Travis without installing it...
Feedback bjoelle:
has_unique_ids: the doc of this function implies that it checks both parameter and distribution ids, but get_duplicate_ids only checks real parameters
Re: CRAN submission beastier 2.0.13
23 May 2019 11:56 9 KB
From:
Uwe Ligges
To:
Richèl J.C. Bilderbeek, CRANThanks, can you please add a
SystemRequirements field to the DESCRIPTION file and define BEAST2 (and if applicable a minimal version) that you package apparently needs?Please fix and resubmit.
Best,
Uwe Ligges
Uses do_minimal_run
someway.
The beast2_working_dir
is a beast2_option
that should act as a bunker for whatever BEAST2 does. @thijsjanzen made me realize that there are no errors if the user specifies to store the BEAST2 output files in that folder.
Modify create_beast2_cmd_run
as described here
Currently, beastier
has some special file handling, due to BEAST2's file creation. This would maybe vanish if BEAST2 was run run with pwd
set to a temp folder.
[edit by @richelbilderbeek: this Issue had nothing to do with beastier
]
On a cluster (not peregrine), beastier::install_beast2
fails with:
downloaded 0 bytes
Error in utils::download.file(url = url, destfile = local_path) :
cannot download all files
In addition: Warning message:
In utils::download.file(url = url, destfile = local_path) :
URL 'https://github-production-release-asset-2e65be.s3.amazonaws.com/15949777/195f6580-2aaa-11e9-9ba5-3f6739d075c1?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20190603%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20190603T084329Z&X-Amz-Expires=300&X-Amz-Signature=4835b41670df45c54f9e07df88a37b62212f1903dcf942cd5d7c3b2302aa4605&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DBEAST.v2.5.2.Linux.tgz&response-content-type=application%2Foctet-stream': status was '403 Forbidden'
Currently, BEAST2 is run in the working directory of the user, after which files are moved to temporary paths.
Perhaps using a temporary folder for BEAST2 simplifies things a lot.
Feedback bjoelle:
run_beast2, create_beast2_run_cmd: the doc should mention that rng_seed can be NA and what happens in that case (i.e the seed will be set to random).
An informal request by @thijsjanzen:
Write beastier::get_beast2_version()
to obtain the BEAST2 version
A local-only error:
Error: file.exists(output_log_filename) is not TRUE
In addition: Warning messages:
1: In file.rename(from = from, to = output_log_filename) :
cannot rename file 'test_output_0.log' to '/tmp/RtmpCkIwGP/file1ef65a706c8.log', reason 'Invalid cross-device link'
2: In file.rename(from = from, to = to) :
Show Traceback
Rerun with Debug
Error: file.exists(output_log_filename) is not TRUE
Hypothesis: currently, I have two installations of Lubuntu on my HDD. I think the one tmp
folder is of the other and older Lubuntu version.
Experiment: re-install Lubuntu on the full HDD and it may be solved.
Feedback bjoelle:
is_beast2_input_file
: l38-40 should be removed - they don't do anything and status_code is 0 even if the file is invalid
On MacOS Sierra 10.13.4 I get:
beastier::install_beast2()
downloaded 0 bytesError in utils::download.file(url = url, destfile = local_path) :
cannot download all files
In addition: Warning message:
In utils::download.file(url = url, destfile = local_path) :
URL 'https://github-production-release-asset-2e65be.s3.amazonaws.com/15949777/f0f47ba0-fb6e-11e7-98fc-590aa8a9cf5b?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20180511%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20180511T074241Z&X-Amz-Expires=300&X-Amz-Signature=efaecee27d6347c4fe1aca611dd5387496fe377b2c68f1dea67be5f64221b19f&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3DBEAST.v2.4.8.Linux.tgz&response-content-type=application%2Foctet-stream': status was '403 Forbidden'
Write beastier::update_beast2()
to update the current version of BEAST2
Created beastier_on_windows repo.
In ~/.local/share/beast/examples/nexus/
are NEXUS files, in its superfolder XML files.
get_beast2_example_filenames()
that returns a list of the full path to the BEAST2 example filenamesget_beast2_example_filename(filename)
that returns the full path to a BEAST2 example filename, or calls stop if the file is absentFeedback bjoelle:
gives_beast2_warning: This function has a lot of code in common with is_beast2_input_file, so I would suggest putting the common code in a separate function that would be called by both.
An informal feature request by @thijsjanzen.
I think it would be a good idea to:
beastier
write to subfolders of ~/.cache/beastier
beastier::clear_beastier_cache()
test_that("BEAST2 freezes when treelog file already exists", {
skip("Issue 50, Issue #50")
if (!is_beast2_installed()) return()
beast2_xml_filename <- tempfile(
pattern = "beast2_", tmpdir = rappdirs::user_cache_dir(),
fileext = ".xml"
)
beautier::create_beast2_input_file_from_model(
input_filename = beautier::get_fasta_filename(),
output_filename = beast2_xml_filename,
inference_model = beautier::create_test_inference_model(
mcmc = beautier::create_test_mcmc(
screenlog = beautier::create_screenlog(filename = "")
)
)
)
testit::assert(file.exists(beast2_xml_filename))
# First run works fine, takes approx 1 sec on my computer
beastier::run_beast2_from_options(
beastier::create_beast2_options(
input_filename = beast2_xml_filename,
overwrite = FALSE,
verbose = TRUE
)
)
# Second run causes BEAST2 to freeze
beastier::run_beast2_from_options(
beastier::create_beast2_options(
input_filename = beast2_xml_filename,
overwrite = FALSE,
verbose = TRUE
)
)
})
See here.
The command "sudo apt-get install -qq oracle-java8-installer" failed and exited with 1 during
Feedback bjoelle:
gives_beast2_warning
: this doc should link to is_beast2_input_file rather than are_beast2_input_lines since the input is a file in both.
Thanks @thijsjanzen for the bug report!
Re: BEAST op het cluster: nogmaalser
9 August 2019 14:22 111 KB
From: Janzen, T.
Met VERBOSE = TRUE:
inferring alternative trees
/data/p251362/nodeSub/no_extinct/shared/7
working dir updated to:
/home/p251362/.cache/file1d8d62a4db8a/7
[1] "input_filename: /local/tmp/RtmpMFJNhH/file1d8d66a637bd7.xml"
[1] "output_log_filename: alternative.log"
[1] "output_trees_filenames: alternative.trees"
[1] "output_state_filename: /local/tmp/RtmpMFJNhH/file1d8d635b9521a.xml.state"
[1] ""
[2] " BEAST v2.6.0, 2002-2019"
[3] " Bayesian Evolutionary Analysis Sampling Trees"
[4] " Designed and developed by"
[5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"
[6] " "
[7] " Centre for Computational Evolution"
[8] " University of Auckland"
[9] " [email protected]"
[10] " [email protected]"
[11] " "
[12] " Institute of Evolutionary Biology"
[13] " University of Edinburgh"
[14] " [email protected]"
[15] " "
[16] " David Geffen School of Medicine"
[17] " University of California, Los Angeles"
[18] " [email protected]"
[19] " "
[20] " Downloads, Help & Resources:"
[21] " http://beast2.org/"
[22] " "
[23] " Source code distributed under the GNU Lesser General Public License:"
[24] " http://github.com/CompEvol/beast2"
[25] " "
[26] " BEAST developers:"
[27] " Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, "
[28] " Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, "
[29] "Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, "
[30] " Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie"
[31] " "
[32] " Thanks to:"
[33] " Roald Forsberg, Beth Shapiro and Korbinian Strimmer"
[34] ""
[35] "Random number seed: 1565352693439"
[36] ""
[37] "File: file1d8d66a637bd7.xml seed: 1565352693439 threads: 1"
[38] "Loading package BEAST v2.6.0"
[39] "Loading package BEAST v2.6.0"
[40] "Alignment(temp)"
[41] " 100 taxa"
[42] " 1000 sites"
[43] " 1000 patterns"
[44] ""
[45] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"
[46] "TreeLikelihood(treeLikelihood.temp0) uses BeerLikelihoodCore4"
[47] " Alignment(temp): [taxa, patterns, sites] = [100, 1000, 1000]"
[48] "==============================================================================="
[49] "Citations for this model:"
[50] ""
[51] "Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, "
[52] " Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "
[53] " BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. "
[54] " PLoS computational biology 15, no. 4 (2019): e1006650."
[55] ""
[56] "==============================================================================="
[57] "Done!"
[1] "input_filename_full: /local/tmp/RtmpMFJNhH/file1d8d66a637bd7.xml"
[1] "actual_log_filename: /home/p251362/.cache/file1d8d62a4db8a/7/temp.log"
[1] "actual_trees_filenames: /home/p251362/.cache/file1d8d62a4db8a/7/temp.trees"
[1] "output_log_filename_full: /data/p251362/nodeSub/no_extinct/shared/7/alternative.log"
[1] "output_trees_filenames_full: /data/p251362/nodeSub/no_extinct/shared/7/alternative.trees"
[1] "output_state_filename_full: /local/tmp/RtmpMFJNhH/file1d8d635b9521a.xml.state"
[1] ""
[2] " BEAST v2.6.0, 2002-2019"
[3] " Bayesian Evolutionary Analysis Sampling Trees"
[4] " Designed and developed by"
[5] " Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard"
[6] " "
[7] " Centre for Computational Evolution"
[8] " University of Auckland"
[9] " [email protected]"
[10] " [email protected]"
[11] " "
[12] " Institute of Evolutionary Biology"
[13] " University of Edinburgh"
[14] " [email protected]"
[15] " "
[16] " David Geffen School of Medicine"
[17] " University of California, Los Angeles"
[18] " [email protected]"
[19] " "
[20] " Downloads, Help & Resources:"
[21] " http://beast2.org/"
[22] " "
[23] " Source code distributed under the GNU Lesser General Public License:"
[24] " http://github.com/CompEvol/beast2"
[25] " "
[26] " BEAST developers:"
[27] " Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, "
[28] " Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, "
[29] "Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, "
[30] " Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie"
[31] " "
[32] " Thanks to:"
[33] " Roald Forsberg, Beth Shapiro and Korbinian Strimmer"
[34] ""
[35] "Random number seed: 1565352696500"
[36] ""
[37] "File: file1d8d66a637bd7.xml seed: 1565352696500 threads: 1"
[38] "Loading package BEAST v2.6.0"
[39] "Loading package BEAST v2.6.0"
[40] "Alignment(temp)"
[41] " 100 taxa"
[42] " 1000 sites"
[43] " 1000 patterns"
[44] ""
[45] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"
[46] "TreeLikelihood(treeLikelihood.temp0) uses BeerLikelihoodCore4"
[47] " Alignment(temp): [taxa, patterns, sites] = [100, 1000, 1000]"
[48] "==============================================================================="
[49] "Citations for this model:"
[50] ""
[51] "Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, "
[52] " Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "
[53] " BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. "
[54] " PLoS computational biology 15, no. 4 (2019): e1006650."
[55] ""
[56] "==============================================================================="
[57] "Done!"
[1] "cmd: /apps/generic/software/Java/1.8.0_192/jre/bin/java -jar '/home/p251362/.local/share/beast/lib/launcher.jar' -seed 1565352623.58915 -statefile \"/local/tmp/RtmpMFJNhH/file1d8d635b9521a.xml.state\" -overwrite \"/local/tmp/RtmpMFJNhH/file1d8d66a637bd7.xml\""
Error in beastier::run_beast2(input_filename = beast2_input_filename, :
BEAST2 .log file not created at '/home/p251362/.cache/file1d8d62a4db8a/7/temp.log'
Maybe no permission to write at that location?
Calls: infer_phylogeny -> <Anonymous> -> bbt_run -> <Anonymous>
In addition: Warning messages:
1: In regularize.values(x, y, ties, missing(ties)) :
collapsing to unique 'x' values
2: In system2(command = cmd[1], args = cmd[-1], stdout = TRUE, stderr = TRUE) :
running command ''/apps/generic/software/Java/1.8.0_192/jre/bin/java' -jar '/home/p251362/.local/share/beast/lib/launcher.jar' -seed 1565352623.58915 -statefile "/local/tmp/RtmpMFJNhH/file1d8d635b9521a.xml.state" -overwrite "/local/tmp/RtmpMFJNhH/file1d8d66a637bd7.xml" 2>&1' had status 1
Execution halted
Feedback bjoelle:
run_beast2, create_beast2_run_cmd: the -overwrite option for BEAST2 is not for overwriting the state file (it will always be overwritten), it is for overwriting the log & trees files. Thus at the moment setting overwrite_state_file does nothing (it's also always set back to TRUE at l107 in run_beast2).
Calls remote::install_github
on all beastier
friends, which are tracerer and beautier
From CRAN build log:
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
Author: ‘Richèl J.C. Bilderbeek <[email protected]>’
Authors@R: ‘Richèl J.C. Bilderbeek [aut, cre] (<https://orcid.org/0000-0003-1107-7049>), Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209), David Winter [rev] (David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209)’
For older user that need to update.
Feedback bjoelle:
run_beast2: I think that this function should give a warning before erasing beast_log_filename and beast_trees_filenames if they exist, because I wouldn't have expected those files to be touched at all if I have specified different values for output_log_filename and output_trees_filenames. A better solution would be to move/rename these files temporarily if they already exist, and restore them once the run is done.
Fails due to sed
having another user interface on Mac
(No subject)
2 November 2018 17:10 3 KB
From:
Rivera Leon, V.E.
To: [...]
Fx pease
https://github.com/richelbilderbeek/beastier/blob/3c9a43fa58df11133b3d9417b93800ad40ee5e59/R/is_beast2_input_file.R#L40
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