poonlab/clmp

Genetic clustering with Markov-modulated Poisson processes

clmp's Issues

igraph_neighborhood

I'm running C-igraph version 0.7.1 on Ubuntu, but there's a newer version on the Mac where igraph_neighborhood has 6 arguments instead of 5. This was changed by the developers in 2014. It seems that at some point I installed a newer version of C-igraph on the Mac.

Solution: don't support beta version of igraph.

ape thinks RAxML trees are rooted

> t1 <- read.tree('RAxML_bestTree.fastTrans_9.raxml')
> is.rooted(t1)
[1] TRUE

but BioPython disagrees:

>>> from Bio import Phylo
>>> t = Phylo.read('RAxML_bestTree.fastTrans_9.raxml', 'newick')
>>> t.rooted
False

warning ? ConditionNumber

Hello!!

I am using the clmp in the a mac OS X Yosemite (10.10.5) and R version 3.3.3.

Running the command clmp(tree, nrates = 2) I get the following warning for some of my trees:
Example1: ConditionNumber: maximal condition number 9.01e+12 reached. maxEW=7.75e-04,minEW=7.80e-17,maxdiagC=4.37e-04,mindiagC=2.48e-09

Example2: ConditionNumber: maximal condition number 9.01e+12 reached. maxEW=8.21e-03,minEW=7.58e-16,maxdiagC=1.00e-02,mindiagC=4.72e-16

I get similar message if I use nrates = 3.
I am treating it as a warning, because the analysis does not stop. Should I be worried about it?
And please let me know if you need more information.

Error when compiling clmp with igraph being built from source

I built igraph from source, but when running R CMD INSTALL clmp I get the following error message:

Error: package or namespace load failed for ‘clmp’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/tng92/R/x86_64-pc-linux-gnu-library/3.4/clmp/libs/clmp.so':
  libigraph.so.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/tng92/R/x86_64-pc-linux-gnu-library/3.4/clmp’

I managed to reproduce this error on @gtng92 machine. On the bright side the fix is simple, running sudo ldconfig fixes the problem.

Clean up repo

There's a lot of automake-related files that probably shouldn't be in the repo

File input

Warning: Error in scan: 'file' must be a character string or connection
  216: stop
  215: scan
  214: read.tree
  213: eventReactiveHandler [/home/art/git/clmp/app.R#66]
  211: handlerFunc
  198: func
  196: f
  195: Reduce
  186: do
  185: hybrid_chain
  184: <reactive:eventReactive(input$nwkFile)>
  183: .func
  180: contextFunc
  179: env$runWith
  172: ctx$run
  171: self$.updateValue
  169: v
  167: renderPlot [/home/art/git/clmp/app.R#72]
  165: func
  125: drawPlot
  111: <reactive:plotObj>
   95: drawReactive
   82: origRenderFunc
   81: output$clmpPlot
    1: runApp

midpoint() has problems with bootstrap values

> t3r <- midpoint(t3)
Error in addConfidences.phylo(tree, oldtree) : 
  could not find function "addConfidences.phylo"

Make Shiny!

User unable to install clmp on Ubuntu 16.04

User followed installation instructions but ran into this error message:

* installing to library ‘/home/art/R/x86_64-pc-linux-gnu-library/3.4’
* installing *source* package ‘clmp’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix -map=/build/r-base-AitvI6/r-base-3.4.4=. -fstack-protector-string -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c clmpR.c -o clmpR.o
clmpR.c:1:10: fatal error: igraph.h: No such file or directory

Ubuntu apt installs igraph.h to /usr/include/igraph. This path is in the configure.ac file, but this isn't getting propagated to the command for compiling clmpR.c. I was able to reproduce this error on my workstation, and compiled clmpR.c with this modified command:

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c clmpR.c -o clmpR.o -I/usr/include/igraph

Implement smoothing method

clmp works better on NJ trees than ML trees, where the latter tends to contain more zero or near-zero branch lengths. This seems to prevent the MMPP model from fitting properly. We could use a method such as non parametric rate smoothing to adjust ML tree inputs. Of course this should be validated by simulation.

Implement midpoint rooting function

right now we're using the midpoint function from the package phangorn. This is kind of overkill because this package depends on igraph which is massive. Plus, I haven't been able to install R igraph on Ubuntu:

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.1\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c foreign-graphml.c -o foreign-graphml.o
foreign-graphml.c: In function ‘igraph_write_graph_graphml’:
foreign-graphml.c:1408:46: error: expected ‘)’ before ‘GRAPHML_NAMESPACE_URI’
   ret=fprintf(outstream, "<graphml xmlns=\"" GRAPHML_NAMESPACE_URI "\"\n");
                                              ^
foreign-graphml.c:1412:59: error: expected ‘)’ before ‘GRAPHML_NAMESPACE_URI’
   ret=fprintf(outstream, "         xsi:schemaLocation=\"" GRAPHML_NAMESPACE_URI "\n");
                                                           ^
foreign-graphml.c:1414:38: error: expected ‘)’ before ‘GRAPHML_NAMESPACE_URI’
   ret=fprintf(outstream, "         " GRAPHML_NAMESPACE_URI "/1.0/graphml.xsd\">\n");
                                      ^
/usr/lib/R/etc/Makeconf:134: recipe for target 'foreign-graphml.o' failed
make: *** [foreign-graphml.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/home/art/R/x86_64-pc-linux-gnu-library/3.2/igraph’

Since we're only using one small function, we should re-implement midpoint rooting (which is a fairly simple method) and drop phangorn as a dependency.

Failed to build package

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/clmp/libs/clmp.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/clmp/libs/clmp.so, 6): Symbol not found: _cmaes_GetPtr
  Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/clmp/libs/clmp.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.3/Resources/library/clmp/libs/clmp.so
Error: loading failed
Execution halted

Problem reading in tree from MASTER

> t2 <- read.tree('example.nwk')
Error in if (z[i]) { : missing value where TRUE/FALSE needed

Here is the tree:

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Update INSTALL.md

Attempting to install on Ubuntu 16.04, R 3.4.4

• Bioconductor installation method has changed
• ggrepel requires igraph library:

g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ggrepel.so RcppExports.o repel_boxes.o -lgsl -ligraph -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -ligraph

clmp app dropping connection with "Disconnected from the server"

JavaScript console:

Failed to load resource: the server responded with a status of 404 (Not Found)
shiny-server-client.min.js:1 Thu Jun 20 2019 15:05:05 GMT-0400 (Eastern Daylight Time) [INF]: Connection opened. http://filogeneti.ca:3838/clmp/
shiny-server-client.min.js:1 Thu Jun 20 2019 15:05:05 GMT-0400 (Eastern Daylight Time) [DBG]: Open channel 0
shiny-server-client.min.js:1 The application unexpectedly exited.

Diagnostic information is private. Please ask your system admin for permission if you need to check the R logs.
shiny-server-client.min.js:1 Thu Jun 20 2019 15:05:06 GMT-0400 (Eastern Daylight Time) [INF]: Connection closed. Info: {"type":"close","code":4503,"reason":"The application unexpectedly exited","wasClean":true}
shiny-server-client.min.js:1 Thu Jun 20 2019 15:05:06 GMT-0400 (Eastern Daylight Time) [DBG]: SockJS connection closed
shiny-server-client.min.js:1 Thu Jun 20 2019 15:05:06 GMT-0400 (Eastern Daylight Time) [DBG]: Channel 0 is closed
shiny-server-client.min.js:1 Thu Jun 20 2019 15:05:06 GMT-0400 (Eastern Daylight Time) [DBG]: Removed channel 0, 0 left

Set up SSL

https://certbot.eff.org/lets-encrypt/ubuntuxenial-apache

Make return value of clmp into an S3 object with nice print and summary functions

Also the plot function can be used to display the tree with branches colored with respect to clusters

Point subdomain shiny.filogeneti.ca to port 3838

In /etc/apache2:

• added file sites-enabled/shiny.conf with ServerName shiny.filogeneti.ca
• uncommented <Directory /srv/> block in apache2.conf
• enabled mod_proxy
• enabled mod_proxy_http
• restarted apache

Directing browser to this URL results in a DNS_PROBE_FINISHED_NXDOMAIN error.

Check log-likelihood calculations and interpretation

I obtained these results on a simulated tree with 500 tips where there was assumed to be two risk groups with a transmission rate discordance by a factor of 3.

> res <- clmp(t1, nrates=1)
log likelihood for 1 state model is 898.696965
rates: 185.511109 
Q: [    *    ]
> res <- clmp(t1, nrates=2)
log likelihood for 2 state model is 903.303757
rates: 170.256368 481.467315 
Q: [    *   2.990365 ]
   [ 6.715851   *    ]
> table(res)
res
  0   1 
904  79 
> res <- clmp(t1, nrates=3)
ConditionNumber: maximal condition number 9.01e+12 reached. maxEW=1.87e-02,minEW=1.93e-15,maxdiagC=1.16e-02,mindiagC=2.48e-15
log likelihood for 3 state model is 903.801291
rates: 74.498138 180.094874 484.310980 
Q: [    *   0.00000046.299770 ]
   [ 7.564244   *   0.000000 ]
   [ 0.0000008.826223   *    ]
> table(res)
res
  1 
983 

Remove flex and bison dependencies

Need to make a different Newick parser.

Installation with devtools::install_github

Attempting to re-install clmp from GitHub via:

devtools::install_github("PoonLab/clmp")

results in following error

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/clmp/libs/clmp.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/clmp/libs/clmp.so, 6): Symbol not found: _gsl_odeiv2_step_rkf45
  Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/clmp/libs/clmp.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/3.3/Resources/library/clmp/libs/clmp.so

Shiny app should update outputs progressively

Currently waits until all analyses completed before displaying outputs.
For instance, I'd like for the app to plot the tree before attempting to fit the clmp models.

Write documentation!

Shiny: add usage tracking

https://shiny.rstudio.com/articles/usage-metrics.html

Bioconductor installation method changed for R 3.6+

> source("https://bioconductor.org/biocLite.R")
 Error in eval(quote({ : 
  With R version 3.6 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install 

Make R function for plotting tree with cluster assignments

Use ggtree

Corrupt data

At commit 52dd6a2

art@Kestrel:~/git/clmp$ R CMD INSTALL .
* installing to library ‘/home/art/R/x86_64-pc-linux-gnu-library/3.4’
* installing *source* package ‘clmp’ ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make: Nothing to be done for 'all'.
installing to /home/art/R/x86_64-pc-linux-gnu-library/3.4/clmp/libs
** R
** data
*** moving datasets to lazyload DB
Warning: file ‘structSIR.RData’ has magic number 'RDX3'
  Use of save versions prior to 2 is deprecated
Error in load(zfile, envir = envir) : 
  bad restore file magic number (file may be corrupted) -- no data loaded
ERROR: lazydata failed for package ‘clmp’
* removing ‘/home/art/R/x86_64-pc-linux-gnu-library/3.4/clmp’
* restoring previous ‘/home/art/R/x86_64-pc-linux-gnu-library/3.4/clmp’

Similarly:

> load('data/structSIR.RData')
Error in load("data/structSIR.RData") : 
  bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘structSIR.RData’ has magic number 'RDX3'
  Use of save versions prior to 2 is deprecated 

Get C function `clmpR` to return ML estimates of rate parameters

Currently they are just being printed to stderr.
It would also be nice to get the log-likelihood returned.

Shiny app needs to handle ML trees

Either let the user specify that the tree was reconstructed by ML and provide the sequence length, or (preferably) automatically detect near-zero branch lengths.

plot function not working

> plot(res)
Error in UseMethod("as.phylo") : 
  no applicable method for 'as.phylo' applied to an object of class "c('clmp', 'phylo')"

This seems to be associated with the initial call to ggtree::fortify

Shiny app needs to check inputs

Presently console spills the following if an arbitrary string is input in text field:

Warning: Error in FUN: object 'node' not found
  183: FUN
  182: lapply
  181: scales_add_defaults
  180: f
  179: l$compute_aesthetics
  178: f
  177: by_layer
  176: ggplot_build.ggplot
  174: print.ggplot
  166: func
  164: f
  163: Reduce
  154: do
  153: hybrid_chain
  125: drawPlot
  111: <reactive:plotObj>
   95: drawReactive
   82: origRenderFunc
   81: output$clmpPlot
    1: runApp
Warning: Error in clmp: argument <tree> must be of class character, phylo or multiphylo
  98: stop
  97: clmp
  96: renderText [/home/art/git/clmp/app.R#57]
  95: func
  82: origRenderFunc
  81: output$loglik1
   1: runApp
Warning: Error in clmp: argument <tree> must be of class character, phylo or multiphylo
  98: stop
  97: clmp
  96: renderText [/home/art/git/clmp/app.R#62]
  95: func
  82: origRenderFunc
  81: output$loglik2
   1: runApp

Installation in Ubuntu

Attempting a fresh install of netabc on an Ubuntu workstation; writing this issue to track what I needed to install. Taking a naive approach (without reading the installation instructions :-) )

1. git clone --recursive http://github.com/PoonLab/netabc
2. apt install libgsl-dev
3. apt install libjudy-dev
4. apt install libyaml-dev
5. apt install check
6. aclocal-1.14 is missing on your system; this workstation's aclocal is newer (1.15). Ran bash autogen.sh
7. Error when attempting to run make:
   ../build-aux/ylwrap: line 176: yacc: command not found
   I forgot to install bison! Interesting the configure script doesn't check for this.
   apt install bison
8. Forgot to install flex as well 😞
   apt install flex
9. This one's interesting!

gcc: error: ./foreign-ncol-lexer.c: No such file or directory 
gcc: fatal error: no input files
compilation terminated.

Needed to enter igraph directory and run ./configure; make; sudo make install

10. Another interesting bug:

In file included from mmpp.c:12:0:
mmpp.h:9:27: fatal error: igraph/igraph.h: No such file or directory

This file is in igraph/include/igraph.h. Changed the affected header line in mmpp.h accordingly.

11. Sigh:

gcc: error: ./newick_lexer.c: No such file or directory
gcc: fatal error: no input files

Realized that I forgot the -enable-tls flag when calling ./configure. On entering this, the
system recompiled igraph and complained about being unable to find -lgmp or -lxml2, so I
installed libgmp-dev and libxml2-dev via apt. Finally successfully compiled!

Problem finding igraph during installation

After running "make", igraph was not found.

mac install fix

For Mac users, you may have to edit the Makevars file before running 'R CMD INSTALL clmp'
and replace -lfl by -ll as follow:
PKG_LIBS = -ligraph -L/usr/local/lib -L/opt/local/lib -lgsl -ll

It works fine with me.
thank you for this great tool!

Add R wrapper for mmpp

Added src/clmpR.c and mimicked the R wrappers we wrote for PoonLab/Kaphi
Need to get this to compile with the rest of the package

Clean up files

c-cmaes is creating two files:

• actparcmaes.par
• errcmaes.err

If these are not required, we should either not output them or remove them once the analysis is complete.

Cannot get index.Rmd and keep clmp app online

If I have the shiny-server load the file index.Rmd at the root directory /srv/shiny-server, it will render the HTML but the clmp app is broken. The app returns to normal when I rename this file to index.Rmd.bak.

move c-cmaes source files back to subdir

Installation raises the following error:

art@orolo:~/git/clmp$ R CMD INSTALL .
* installing to library ‘/home/art/R/x86_64-pc-linux-gnu-library/3.6’
* installing *source* package ‘clmp’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c clmpR.c -o clmpR.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c midpoint_help.cpp -o midpoint_help.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mmpp.c -o mmpp.o
mmpp.c: In function ‘guess_parameters’:
mmpp.c:231:14: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         edge = igraph_inclist_get(&il, i);
              ^
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c newick_lexer.c -o newick_lexer.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c newick_parser.c -o newick_parser.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stats.c -o stats.o
stats.c: In function ‘parse_distribution’:
stats.c:176:9: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration]
     if (strcmp(s, "uniform") == 0) {
         ^~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tree.c -o tree.o
tree.c:14:0: warning: "NDEBUG" redefined
 #define NDEBUG
 
<command-line>:0:0: note: this is the location of the previous definition
tree.c: In function ‘_permute_tree_attrs’:
tree.c:287:13: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         inc = igraph_inclist_get(&inclist, i);
             ^
tree.c: In function ‘subsample’:
tree.c:701:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                 inc = igraph_inclist_get(&inclist, v);
                     ^
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/opt/local/include -I/usr/local/include -I/usr/include/igraph -I"/home/art/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include"   -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-VjHo9C/r-base-3.6.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c util.c -o util.o
util.c: In function ‘sample_weighted’:
util.c:217:9: warning: implicit declaration of function ‘gsl_ran_choose’; did you mean ‘gsl_rng_clone’? [-Wimplicit-function-declaration]
         gsl_ran_choose(rng, dest, k, x, n, size);
         ^~~~~~~~~~~~~~
         gsl_rng_clone
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o clmp.so RcppExports.o clmpR.o midpoint_help.o mmpp.o newick_lexer.o newick_parser.o stats.o tree.o util.o -ligraph -L/usr/local/lib -L/opt/local/lib -lgsl -lfl -L/usr/lib/R/lib -lR
installing to /home/art/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-clmp/00new/clmp/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘clmp’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/art/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-clmp/00new/clmp/libs/clmp.so':
  /home/art/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-clmp/00new/clmp/libs/clmp.so: undefined symbol: cmaes_boundary_transformation_init
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/art/R/x86_64-pc-linux-gnu-library/3.6/clmp’
* restoring previous ‘/home/art/R/x86_64-pc-linux-gnu-library/3.6/clmp’

Compile newick_parser

Currently we're carrying around these files:

• newick_parser.c
• newick_parser.h
• newick_lexer.c

These were generated from the source files newick_lexer.l and newick_parser.y ages ago and we've had a difficult time reproducing this process since. Unfortunately this is a problem for making a portable distribution.

I have been able to compile the above source files in Ubuntu 18.04 as follows:

bison -d newick_parser.y
flex newick_lexer.l
gcc newick_parser.tab.c lex.yy.c -lfl -lm -ligraph

which yields the default binary a.out.

How do we generate the .c and .h files mentioned at the top of this post?

Ambiguous reporting of rate class assignments

If we fit two rate classes, then branches assigned to cluster 0 belong to the background rate class and branches in clusters with indices greater than 0 belong to the second rate class. However, if we fit more than two rate classes then clusters with index greater than 0 could belong to the second, third or additional rate classes.

Installation issue on Ubuntu 16.04 with R 3.4.4

Error: package or namespace load failed for ‘clmp’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/art/R/x86_64-pc-linux-gnu-library/3.4/clmp/libs/clmp.so':
  /home/art/R/x86_64-pc-linux-gnu-library/3.4/clmp/libs/clmp.so: undefined symbol: gsl_rng_default
Error: loading failed

Stochastic stalling of clmp call on 100-tip tree

clmp function sometimes outputs results with a 100-tip tree, and other times seems to enter an infinite loop.

clmp is crashed on test tree of 1000 tips

Needed to recompile /src folder.

Run through examples to verify installation

Unable to install dependency ggtree

> biocLite("ggtree")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.3 (2019-03-11).
Installing package(s) ‘ggtree’
trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/ggtree_1.12.7.tar.gz'
Content type 'application/x-gzip' length 5845438 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

* installing *source* package ‘ggtree’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error : object ‘as_data_frame’ is not exported by 'namespace:tidytree'
ERROR: lazy loading failed for package ‘ggtree’
* removing ‘/home/art/R/x86_64-pc-linux-gnu-library/3.5/ggtree’

The downloaded source packages are in
	‘/tmp/Rtmp2zaXpe/downloaded_packages’
installation path not writeable, unable to update packages: lhs,
  boot, cluster, foreign, MASS, nlme, rpart, survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ggtree’ had non-zero exit status

If the C mmpp program gets stuck then it is difficult to terminate the process in R

See if there is a way to make this more user-friendly

Had to remove `-lfl` flag in Makevars

Had to do this for macOS.
Check if package will still build in Linux.

Generate clusters from rate class assignments in R

Involves pre-order traversal

Build directed graph of arguments and return values for functions in netabc

The purpose of this graph is to provide visual documentation of the relationships among functions and libraries in netabc. This will make it easier to modify and integrate this code into the Kamphir project. You can use the DOT language to build the directed graph. Each node should represent a function and each edge represent an argument or return value. Nodes and edges should be labelled with the function and variable names, respectively. Please add the DOT file to the repository.

Give feedback if user tries to run clmp on list of trees

> t2
10 phylogenetic trees
> res <- clmp(t2, nrates=1)
Error in double(nb.tip + nb.node) : invalid 'length' argument
In addition: Warning message:
In if (!is.rooted(tree2)) { :
  the condition has length > 1 and only the first element will be used