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thibautjombart / apex

Phylogenetic Methods for Multiple Gene Data
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Example initialize,multiphyDat-method fails #5

Closed thibautjombart closed 9 years ago

thibautjombart commented 9 years ago

base::assign(".ptime", proc.time(), pos = "CheckExEnv")

Name: initialize,multiphyDat-method

Title: multiphyDat constructor

Aliases: initialize,multiphyDat-method initialize,multiphyDat-methods

\ Examples

empty object

new("multiphyDat") An object of class "multiphyDat" Slot "dna": NULL

Slot "labels": character(0)

Slot "n.ind": [1] 0

Slot "n.seq": [1] 0

Slot "ind.info": NULL

Slot "gene.info": NULL

simple conversion with nicely ordered output

data(Laurasiatherian) genes <- list(gene1=subset(Laurasiatherian,, 1:1600, FALSE), gene2=subset(Laurasiatherian,, 1601:3179, FALSE)) Error in if (all(rows > 0)) attr(data, "weight") = weight else attr(data, : missing value where TRUE/FALSE needed Calls: subset -> subset.phyDat -> getRows Execution halted Error: Command failed (1) In addition: Warning message: package ‘phangorn’ was built under R version 3.2.0

thibautjombart commented 9 years ago

I have \dontrunned the examples in both muldiDat files to pass the check: 6c60c3fd4d7c05 the errors are still there though.

KlausVigo commented 9 years ago

The second example should be fine the first requires the latest phangorn version devtools::install_github("KlausVigo/phangorn")

thibautjombart commented 9 years ago

Just tried but I can't seem to install phangorn's current github version:

> install_github("KlausVigo/phangorn")
Downloading github repo KlausVigo/phangorn@master
Installing phangorn
'/usr/local/lib/R/bin/R' --vanilla CMD INSTALL  \
  '/tmp/RtmpORlxbN/devtoolsbb57746c28d/KlausVigo-phangorn-7c6ac41'  \
  --library='/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3'  \
  --install-tests 

* installing *source* package ‘phangorn’ ...
** libs
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/Rcpp/include" -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/RcppArmadillo/include"  -fopenmp -fpic  -g -O2  -c dist.c -o dist.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/Rcpp/include" -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/RcppArmadillo/include"  -fopenmp -fpic  -g -O2  -c fitch.c -o fitch.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/Rcpp/include" -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/RcppArmadillo/include"  -fopenmp -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/Rcpp/include" -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/RcppArmadillo/include"  -fopenmp -fpic  -g -O2  -c ml.c -o ml.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/Rcpp/include" -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/RcppArmadillo/include"  -fopenmp -fpic  -g -O2  -c phangorn.c -o phangorn.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/Rcpp/include" -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/RcppArmadillo/include"  -fopenmp -fpic  -g -O2  -c read_aa.c -o read_aa.o
gcc -std=gnu99 -I/usr/local/lib/R/include -DNDEBUG  -I/usr/local/include -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/Rcpp/include" -I"/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/RcppArmadillo/include"  -fopenmp -fpic  -g -O2  -c sankoff.c -o sankoff.o
gcc -std=gnu99 -shared -L/usr/local/lib -o phangorn.so dist.o fitch.o init.o ml.o phangorn.o read_aa.o sankoff.o -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp
installing to /home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/phangorn/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Ancestral.Rnw’ 
   ‘Trees.Rnw’ 
   ‘phangorn-specials.Rnw’ 
   ‘Networx.Rmd’ 
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/phangorn/libs/phangorn.so':
  /home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/phangorn/libs/phangorn.so: undefined symbol: fhm
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/thibaut/R/x86_64-unknown-linux-gnu-library/3.3/phangorn’
Error: Command failed (1)

Here's my R version:

> R.version
               _                                                 
platform       x86_64-unknown-linux-gnu                          
arch           x86_64                                            
os             linux-gnu                                         
system         x86_64, linux-gnu                                 
status         Under development (unstable)                      
major          3                                                 
minor          3.0                                               
year           2015                                              
month          03                                                
day            19                                                
svn rev        68032                                             
language       R                                                 
version.string R Under development (unstable) (2015-03-19 r68032)
nickname       Unsuffered Consequences     

> sessionInfo()
R Under development (unstable) (2015-03-19 r68032)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] devtools_1.7.0

loaded via a namespace (and not attached):
[1] httr_0.6.1     formatR_1.0    tools_3.3.0    RCurl_1.95-4.5 knitr_1.9     
[6] stringr_0.6.2  bitops_1.0-6   evaluate_0.5.5
KlausVigo commented 9 years ago

Should work now.

thibautjombart commented 9 years ago

Yep! :) I'm closing the issue. Thanks!