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ropensci / beastier

R package to run BEAST2
https://docs.ropensci.org/beastier
GNU General Public License v3.0
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BEAST2 .log file not created #35

Closed richelbilderbeek closed 5 years ago

richelbilderbeek commented 5 years ago

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] "                       r.bouckaert@auckland.ac.nz"                               

[10] "                        alexei@cs.auckland.ac.nz"                                

[11] "                                    "                                            

[12] "                   Institute of Evolutionary Biology"                            

[13] "                        University of Edinburgh"                                 

[14] "                           a.rambaut@ed.ac.uk"                                   

[15] "                                    "                                            

[16] "                    David Geffen School of Medicine"                             

[17] "                 University of California, Los Angeles"                          

[18] "                           msuchard@ucla.edu"                                    

[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] "                       r.bouckaert@auckland.ac.nz"                               

[10] "                        alexei@cs.auckland.ac.nz"                                

[11] "                                    "                                            

[12] "                   Institute of Evolutionary Biology"                            

[13] "                        University of Edinburgh"                                 

[14] "                           a.rambaut@ed.ac.uk"                                   

[15] "                                    "                                            

[16] "                    David Geffen School of Medicine"                             

[17] "                 University of California, Los Angeles"                          

[18] "                           msuchard@ucla.edu"                                    

[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
richelbilderbeek commented 5 years ago

Breaking down the bug report, there are four things to do:

1: In regularize.values(x, y, ties, missing(ties)) :

  collapsing to unique 'x' values

This error message is irrelevant to this Issue

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
richelbilderbeek commented 5 years ago

From @thijsjanzen:

Ik start het bijgevoegde script in

/home/p251362/nodeSub/no_extinct/shared/1/

Of in /data/p251362/nodeSub/no_extinct/shared/1/

Om het script te laten werken, eerst: devtools::install_github("thijsjanzen/nodeSub")

cluster_twin.zip

Great, I can work with that!

richelbilderbeek commented 5 years ago

Already running locally:

[1] "input_filename_full: /home/richel/.cache/file609a170e49dc/file609a20c622aa.xml"
[1] "actual_log_filename: /home/richel/GitHubs/beastier/temp.log"
[1] "actual_trees_filenames: /home/richel/GitHubs/beastier/temp.trees"
[1] "output_log_filename_full: /home/richel/GitHubs/beastier/alternative.log"
[1] "output_trees_filenames_full: /home/richel/GitHubs/beastier/alternative.trees"
[1] "output_state_filename_full: /home/richel/.cache/file609a680e1edf/file609a337af738.xml.state"
Error in beastier::run_beast2(input_filename = beast2_input_filename,  : 
  log file to be created '/home/richel/GitHubs/beastier/temp.log' is already present. 
This should never happen. 
If you have a reproducible example, please post a bug report at https://github.com/ropensci/beastier/issues 
Called from: beastier::run_beast2(input_filename = beast2_input_filename, 
    rng_seed = rng_seed, output_log_filename = beast2_output_log_filename, 
    output_trees_filenames = beast2_output_trees_filenames, output_state_filename = beast2_output_state_filename, 
    beast2_working_dir = beast2_working_dir, beast2_path = beast2_path, 
    overwrite = overwrite, verbose = verbose)
Browse[1]> Q

This means that a local filename (i.e. without a unique complete path) is re-used, which may be related to the mcbette Issue 10.

Definitely this is the error message that should have shown up in the earlier examples!

richelbilderbeek commented 5 years ago

Also the Peregrine log file:


The following have been reloaded with a version change:
  1) GCCcore/7.3.0 => GCCcore/4.9.3

The following have been reloaded with a version change:
  1) FFTW/3.3.7-gompi-2018a => FFTW/3.3.4-gompi-2016a
  2) GCC/6.4.0-2.28 => GCC/4.9.3-2.25
  3) OpenBLAS/0.2.20-GCC-6.4.0-2.28 => OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0
  4) OpenMPI/2.1.2-GCC-6.4.0-2.28 => OpenMPI/1.10.3-GCC-4.9.3-2.25
  5) ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20 => ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0
  6) XZ/5.2.3-GCCcore-6.4.0 => XZ/5.2.2-foss-2016a
  7) binutils/2.28-GCCcore-6.4.0 => binutils/2.25-GCCcore-4.9.3
  8) gompi/2018a => gompi/2016a
  9) hwloc/1.11.8-GCCcore-6.4.0 => hwloc/1.11.2-GCC-4.9.3-2.25
 10) numactl/2.0.11-GCCcore-6.4.0 => numactl/2.0.11-GCC-4.9.3-2.25

The following have been reloaded with a version change:
  1) FFTW/3.3.4-gompi-2016a => FFTW/3.3.7-gompi-2018a
  2) GCC/4.9.3-2.25 => GCC/6.4.0-2.28
  3) GCCcore/4.9.3 => GCCcore/6.4.0
  4) OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0 => OpenBLAS/0.2.20-GCC-6.4.0-2.28
  5) OpenMPI/1.10.3-GCC-4.9.3-2.25 => OpenMPI/2.1.2-GCC-6.4.0-2.28
  6) ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0 => ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20
  7) XZ/5.2.2-foss-2016a => XZ/5.2.3-GCCcore-6.4.0
  8) binutils/2.25-GCCcore-4.9.3 => binutils/2.28-GCCcore-6.4.0
  9) foss/2016a => foss/2018a
 10) gompi/2016a => gompi/2018a
 11) hwloc/1.11.2-GCC-4.9.3-2.25 => hwloc/1.11.8-GCCcore-6.4.0
 12) numactl/2.0.11-GCC-4.9.3-2.25 => numactl/2.0.11-GCCcore-6.4.0
 13) zlib/1.2.11-GCCcore-7.3.0 => zlib/1.2.11-GCCcore-6.4.0

The following have been reloaded with a version change:
  1) Ghostscript/9.23-GCCcore-6.4.0 => Ghostscript/9.22-GCCcore-6.4.0-cairo-1.14.12
  2) ImageMagick/6.9.10-5-GCCcore-6.4.0 => ImageMagick/7.0.7-26-foss-2018a
  3) LittleCMS/2.9-GCCcore-6.4.0 => LittleCMS/2.9-foss-2018a
  4) expat/2.2.5-GCCcore-7.3.0 => expat/2.2.5-GCCcore-6.4.0

Rscript issue_35.R
Downloading GitHub repo thijsjanzen/nodeSub@master
testthat    (2.1.1        -> 2.2.1       ) [CRAN]
apTreeshape (NA           -> 1.5-0       ) [CRAN]
pbapply     (1.4-0        -> 1.4-1       ) [CRAN]
TreeSim     (NA           -> 2.4         ) [CRAN]
peregrine   (5570cd816... -> c63daf57e...) [GitHub]
quantreg    (5.41         -> 5.51        ) [CRAN]
Installing 5 packages: testthat, apTreeshape, pbapply, TreeSim, quantreg
Installing packages into ‘/home/p230198/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/testthat_2.2.1.tar.gz'
Content type 'application/x-gzip' length 235874 bytes (230 KB)
==================================================
downloaded 230 KB

trying URL 'https://cloud.r-project.org/src/contrib/apTreeshape_1.5-0.tar.gz'
Content type 'application/x-gzip' length 54359 bytes (53 KB)
==================================================
downloaded 53 KB

trying URL 'https://cloud.r-project.org/src/contrib/pbapply_1.4-1.tar.gz'
Content type 'application/x-gzip' length 15130 bytes (14 KB)
==================================================
downloaded 14 KB

trying URL 'https://cloud.r-project.org/src/contrib/TreeSim_2.4.tar.gz'
Content type 'application/x-gzip' length 31585 bytes (30 KB)
==================================================
downloaded 30 KB

trying URL 'https://cloud.r-project.org/src/contrib/quantreg_5.51.tar.gz'
Content type 'application/x-gzip' length 995236 bytes (971 KB)
==================================================
downloaded 971 KB

* installing *source* package ‘testthat’ ...
** package ‘testthat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c init.c -o init.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c reassign.c -o reassign.o
g++ -std=gnu++11 -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c test-catch.cpp -o test-catch.o
g++ -std=gnu++11 -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c test-example.cpp -o test-example.o
g++ -std=gnu++11 -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT  -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++11 -shared -L/software/software/R/3.6.1-foss-2018a/lib64/R/lib -L/software/software/GCCcore/6.4.0/lib64 -L/software/software/GCCcore/6.4.0/lib -L/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib -L/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/lib -L/software/software/FFTW/3.3.7-gompi-2018a/lib -L/software/software/X11/20180131-GCCcore-6.4.0/lib -L/software/software/Mesa/17.3.6-foss-2018a/lib -L/software/software/libGLU/9.0.0-foss-2018a/lib -L/software/software/cairo/1.14.12-GCCcore-6.4.0/lib -L/software/software/libreadline/7.0-GCCcore-6.4.0/lib -L/software/software/ncurses/6.1-GCCcore-6.4.0/lib -L/software/software/bzip2/1.0.6-GCCcore-6.4.0/lib -L/software/software/XZ/5.2.3-GCCcore-6.4.0/lib -L/software/software/zlib/1.2.11-GCCcore-6.4.0/lib -L/software/software/SQLite/3.21.0-GCCcore-6.4.0/lib -L/software/software/PCRE/8.41-GCCcore-6.4.0/lib -L/software/software/libpng/1.6.34-GCCcore-6.4.0/lib -L/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/lib -L/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/lib -L/software/software/Java/1.8.0_192/lib -L/software/software/Tk/8.6.8-foss-2018a/lib -L/software/software/cURL/7.58.0-GCCcore-6.4.0/lib -L/software/software/libxml2/2.9.7-GCCcore-6.4.0/lib -L/software/software/GMP/6.1.2-GCCcore-6.4.0/lib -L/software/software/NLopt/2.4.2-foss-2018a/lib -L/software/software/libsndfile/1.0.28-GCCcore-6.4.0/lib -L/software/software/ICU/61.1-GCCcore-6.4.0/lib -L/software/software/HDF5/1.10.1-foss-2018a/lib -L/software/software/UDUNITS/2.2.26-foss-2018a/lib -L/software/software/GSL/2.4-GCCcore-6.4.0/lib -L/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/lib -o testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o -L/software/software/R/3.6.1-foss-2018a/lib64/R/lib -lR
installing to /home/p230198/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-testthat/00new/testthat/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (testthat)
* installing *source* package ‘pbapply’ ...
** package ‘pbapply’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pbapply)
* installing *source* package ‘TreeSim’ ...
** package ‘TreeSim’ successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TreeSim)
* installing *source* package ‘quantreg’ ...
** package ‘quantreg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c boot.f -o boot.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c bound.f -o bound.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c boundc.f -o boundc.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c brute.f -o brute.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c chlfct.f -o chlfct.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c cholesky.f -o cholesky.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c combos.f -o combos.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c crqf.f -o crqf.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c crqfnb.f -o crqfnb.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c dsel05.f -o dsel05.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c etime.f -o etime.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c extract.f -o extract.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c idmin.f -o idmin.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c iswap.f -o iswap.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c kuantiles.f -o kuantiles.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c linpack.f -o linpack.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c mcmb.c -o mcmb.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c penalty.f -o penalty.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c powell.f -o powell.o
gcc -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG   -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c quantreg_init.c -o quantreg_init.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c rls.f -o rls.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c rq0.f -o rq0.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c rq1.f -o rq1.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c rqbr.f -o rqbr.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c rqfn.f -o rqfn.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c rqfnb.f -o rqfnb.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c rqfnc.f -o rqfnc.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c rqs.f -o rqs.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c sakj.f -o sakj.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c sparskit2.f -o sparskit2.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c srqfn.f -o srqfn.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c srqfnc.f -o srqfnc.o
gfortran  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c srtpai.f -o srtpai.o
gcc -shared -L/software/software/R/3.6.1-foss-2018a/lib64/R/lib -L/software/software/GCCcore/6.4.0/lib64 -L/software/software/GCCcore/6.4.0/lib -L/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib -L/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/lib -L/software/software/FFTW/3.3.7-gompi-2018a/lib -L/software/software/X11/20180131-GCCcore-6.4.0/lib -L/software/software/Mesa/17.3.6-foss-2018a/lib -L/software/software/libGLU/9.0.0-foss-2018a/lib -L/software/software/cairo/1.14.12-GCCcore-6.4.0/lib -L/software/software/libreadline/7.0-GCCcore-6.4.0/lib -L/software/software/ncurses/6.1-GCCcore-6.4.0/lib -L/software/software/bzip2/1.0.6-GCCcore-6.4.0/lib -L/software/software/XZ/5.2.3-GCCcore-6.4.0/lib -L/software/software/zlib/1.2.11-GCCcore-6.4.0/lib -L/software/software/SQLite/3.21.0-GCCcore-6.4.0/lib -L/software/software/PCRE/8.41-GCCcore-6.4.0/lib -L/software/software/libpng/1.6.34-GCCcore-6.4.0/lib -L/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/lib -L/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/lib -L/software/software/Java/1.8.0_192/lib -L/software/software/Tk/8.6.8-foss-2018a/lib -L/software/software/cURL/7.58.0-GCCcore-6.4.0/lib -L/software/software/libxml2/2.9.7-GCCcore-6.4.0/lib -L/software/software/GMP/6.1.2-GCCcore-6.4.0/lib -L/software/software/NLopt/2.4.2-foss-2018a/lib -L/software/software/libsndfile/1.0.28-GCCcore-6.4.0/lib -L/software/software/ICU/61.1-GCCcore-6.4.0/lib -L/software/software/HDF5/1.10.1-foss-2018a/lib -L/software/software/UDUNITS/2.2.26-foss-2018a/lib -L/software/software/GSL/2.4-GCCcore-6.4.0/lib -L/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/lib -o quantreg.so boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crqf.o crqfnb.o dsel05.o etime.o extract.o idmin.o iswap.o kuantiles.o linpack.o mcmb.o penalty.o powell.o quantreg_init.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o rqs.o sakj.o sparskit2.o srqfn.o srqfnc.o srtpai.o -lopenblas -lgfortran -lgfortran -lgfortran -L/software/software/R/3.6.1-foss-2018a/lib64/R/lib -lR
installing to /home/p230198/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-quantreg/00new/quantreg/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (quantreg)
* installing *source* package ‘apTreeshape’ ...
** package ‘apTreeshape’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** demo
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (apTreeshape)

The downloaded source packages are in
    ‘/local/tmp/Rtmpf9l8SU/downloaded_packages’
Downloading GitHub repo richelbilderbeek/peregrine@richel

   checking 

   checking for file 

   checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd6720ef5d/richelbilderbeek-peregrine-c63daf5/DESCRIPTION’

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   checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd6720ef5d/richelbilderbeek-peregrine-c63daf5/DESCRIPTION’ ... 

   checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd6720ef5d/richelbilderbeek-peregrine-c63daf5/DESCRIPTION’ ... OK

✔  checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd6720ef5d/richelbilderbeek-peregrine-c63daf5/DESCRIPTION’

─  preparing ‘peregrine’:
   checking DESCRIPTION meta-information ...

   checking DESCRIPTION meta-information ... 

   checking DESCRIPTION meta-information ... OK

✔  checking DESCRIPTION meta-information

   checking for LF line-endings in source and make files and shell scripts

─  checking for LF line-endings in source and make files and shell scripts

   checking for empty or unneeded directories

─  checking for empty or unneeded directories
─  building ‘peregrine_0.4.tar.gz’

Warning:

   Warning: invalid uid value replaced by that for user 'nobody'

Warning:

   Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/home/p230198/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package ‘peregrine’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (peregrine)

   checking 

   checking for file 

   checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd7b3188b5/thijsjanzen-nodeSub-073273f/DESCRIPTION’

   checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd7b3188b5/thijsjanzen-nodeSub-073273f/DESCRIPTION’ ...

   checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd7b3188b5/thijsjanzen-nodeSub-073273f/DESCRIPTION’ ... 

   checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd7b3188b5/thijsjanzen-nodeSub-073273f/DESCRIPTION’ ... OK

✔  checking for file ‘/local/tmp/Rtmpf9l8SU/remotes160fd7b3188b5/thijsjanzen-nodeSub-073273f/DESCRIPTION’

─  preparing ‘nodeSub’:
   checking DESCRIPTION meta-information ...

   checking DESCRIPTION meta-information ... 

   checking DESCRIPTION meta-information ... OK

✔  checking DESCRIPTION meta-information
─  cleaning src

   checking for LF line-endings in source and make files and shell scripts

─  checking for LF line-endings in source and make files and shell scripts

   checking for empty or unneeded directories

─  checking for empty or unneeded directories

   building 

   building ‘nodeSub_0.3.0.tar.gz’

─  building ‘nodeSub_0.3.0.tar.gz’

Warning:

   Warning: invalid uid value replaced by that for user 'nobody'

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   Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/home/p230198/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
* installing *source* package ‘nodeSub’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG  -I"/home/p230198/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/software/software/R/3.6.1-foss-2018a/lib64/R/include" -DNDEBUG  -I"/home/p230198/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/include -I/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/include -I/software/software/FFTW/3.3.7-gompi-2018a/include -I/software/software/X11/20180131-GCCcore-6.4.0/include -I/software/software/Mesa/17.3.6-foss-2018a/include -I/software/software/libGLU/9.0.0-foss-2018a/include -I/software/software/cairo/1.14.12-GCCcore-6.4.0/include -I/software/software/libreadline/7.0-GCCcore-6.4.0/include -I/software/software/ncurses/6.1-GCCcore-6.4.0/include -I/software/software/bzip2/1.0.6-GCCcore-6.4.0/include -I/software/software/XZ/5.2.3-GCCcore-6.4.0/include -I/software/software/zlib/1.2.11-GCCcore-6.4.0/include -I/software/software/SQLite/3.21.0-GCCcore-6.4.0/include -I/software/software/PCRE/8.41-GCCcore-6.4.0/include -I/software/software/libpng/1.6.34-GCCcore-6.4.0/include -I/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/include -I/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/include -I/software/software/Java/1.8.0_192/include -I/software/software/Tk/8.6.8-foss-2018a/include -I/software/software/cURL/7.58.0-GCCcore-6.4.0/include -I/software/software/libxml2/2.9.7-GCCcore-6.4.0/include -I/software/software/GMP/6.1.2-GCCcore-6.4.0/include -I/software/software/NLopt/2.4.2-foss-2018a/include -I/software/software/libsndfile/1.0.28-GCCcore-6.4.0/include -I/software/software/ICU/61.1-GCCcore-6.4.0/include -I/software/software/HDF5/1.10.1-foss-2018a/include -I/software/software/UDUNITS/2.2.26-foss-2018a/include -I/software/software/GSL/2.4-GCCcore-6.4.0/include -I/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/include  -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c getP.cpp -o getP.o
g++ -std=gnu++11 -shared -L/software/software/R/3.6.1-foss-2018a/lib64/R/lib -L/software/software/GCCcore/6.4.0/lib64 -L/software/software/GCCcore/6.4.0/lib -L/software/software/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib -L/software/software/ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20/lib -L/software/software/FFTW/3.3.7-gompi-2018a/lib -L/software/software/X11/20180131-GCCcore-6.4.0/lib -L/software/software/Mesa/17.3.6-foss-2018a/lib -L/software/software/libGLU/9.0.0-foss-2018a/lib -L/software/software/cairo/1.14.12-GCCcore-6.4.0/lib -L/software/software/libreadline/7.0-GCCcore-6.4.0/lib -L/software/software/ncurses/6.1-GCCcore-6.4.0/lib -L/software/software/bzip2/1.0.6-GCCcore-6.4.0/lib -L/software/software/XZ/5.2.3-GCCcore-6.4.0/lib -L/software/software/zlib/1.2.11-GCCcore-6.4.0/lib -L/software/software/SQLite/3.21.0-GCCcore-6.4.0/lib -L/software/software/PCRE/8.41-GCCcore-6.4.0/lib -L/software/software/libpng/1.6.34-GCCcore-6.4.0/lib -L/software/software/libjpeg-turbo/1.5.3-GCCcore-6.4.0/lib -L/software/software/LibTIFF/4.0.9-GCCcore-6.4.0/lib -L/software/software/Java/1.8.0_192/lib -L/software/software/Tk/8.6.8-foss-2018a/lib -L/software/software/cURL/7.58.0-GCCcore-6.4.0/lib -L/software/software/libxml2/2.9.7-GCCcore-6.4.0/lib -L/software/software/GMP/6.1.2-GCCcore-6.4.0/lib -L/software/software/NLopt/2.4.2-foss-2018a/lib -L/software/software/libsndfile/1.0.28-GCCcore-6.4.0/lib -L/software/software/ICU/61.1-GCCcore-6.4.0/lib -L/software/software/HDF5/1.10.1-foss-2018a/lib -L/software/software/UDUNITS/2.2.26-foss-2018a/lib -L/software/software/GSL/2.4-GCCcore-6.4.0/lib -L/software/software/ImageMagick/6.9.10-5-GCCcore-6.4.0/lib -o nodeSub.so RcppExports.o getP.o -L/software/software/R/3.6.1-foss-2018a/lib64/R/lib -lR
installing to /home/p230198/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-nodeSub/00new/nodeSub/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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nodeSub)
── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.2.0     ✔ purrr   0.3.2
✔ tibble  2.1.3     ✔ dplyr   0.8.3
✔ tidyr   0.8.3     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
model =  shared 
work_dir =  /home/p230198/GitHubs/beastier/scripts 
18.5 
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
simulating nodesub alignment
inferring alternative trees
/home/p230198/GitHubs/beastier/scripts 
working dir updated to: 
/home/p230198/GitHubs/beastier/scripts 
[1] "input_filename: /local/tmp/Rtmpf9l8SU/file160fd769ab7b2.xml"
[1] "output_log_filename: alternative.log"
[1] "output_trees_filenames: alternative.trees"
[1] "output_state_filename: /local/tmp/Rtmpf9l8SU/file160fd6f7b1e9b.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] "                       r.bouckaert@auckland.ac.nz"                               
[10] "                        alexei@cs.auckland.ac.nz"                                
[11] "                                    "                                            
[12] "                   Institute of Evolutionary Biology"                            
[13] "                        University of Edinburgh"                                 
[14] "                           a.rambaut@ed.ac.uk"                                   
[15] "                                    "                                            
[16] "                    David Geffen School of Medicine"                             
[17] "                 University of California, Los Angeles"                          
[18] "                           msuchard@ucla.edu"                                    
[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: 1565709214236"                                               
[36] ""                                                                                
[37] "File: file160fd769ab7b2.xml seed: 1565709214236 threads: 1"                      
[38] "Loading package NS v1.1.0"                                                       
[39] "Loading package MODEL_SELECTION v1.5.0"                                          
[40] "Loading package BEAST v2.6.0"                                                    
[41] "Loading package BEASTLabs v1.9.0"                                                
[42] "Loading package BEAST v2.6.0"                                                    
[43] "Alignment(temp)"                                                                 
[44] "  100 taxa"                                                                      
[45] "  1000 sites"                                                                    
[46] "  1000 patterns"                                                                 
[47] ""                                                                                
[48] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"            
[49] "TreeLikelihood(treeLikelihood.temp0) uses BeerLikelihoodCore4"                   
[50] "  Alignment(temp): [taxa, patterns, sites] = [100, 1000, 1000]"                  
[51] "===============================================================================" 
[52] "Citations for this model:"                                                       
[53] ""                                                                                
[54] "Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, "
[55] "  Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "                
[56] "  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. " 
[57] "  PLoS computational biology 15, no. 4 (2019): e1006650."                        
[58] ""                                                                                
[59] "===============================================================================" 
[60] "Done!"                                                                           
[1] "input_filename_full: /local/tmp/Rtmpf9l8SU/file160fd769ab7b2.xml"
[1] "actual_log_filename: /home/p230198/GitHubs/beastier/scripts/temp.log"
[1] "actual_trees_filenames: /home/p230198/GitHubs/beastier/scripts/temp.trees"
[1] "output_log_filename_full: /home/p230198/GitHubs/beastier/scripts/alternative.log"
[1] "output_trees_filenames_full: /home/p230198/GitHubs/beastier/scripts/alternative.trees"
[1] "output_state_filename_full: /local/tmp/Rtmpf9l8SU/file160fd6f7b1e9b.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] "                       r.bouckaert@auckland.ac.nz"                               
[10] "                        alexei@cs.auckland.ac.nz"                                
[11] "                                    "                                            
[12] "                   Institute of Evolutionary Biology"                            
[13] "                        University of Edinburgh"                                 
[14] "                           a.rambaut@ed.ac.uk"                                   
[15] "                                    "                                            
[16] "                    David Geffen School of Medicine"                             
[17] "                 University of California, Los Angeles"                          
[18] "                           msuchard@ucla.edu"                                    
[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: 1565709217567"                                               
[36] ""                                                                                
[37] "File: file160fd769ab7b2.xml seed: 1565709217567 threads: 1"                      
[38] "Loading package NS v1.1.0"                                                       
[39] "Loading package MODEL_SELECTION v1.5.0"                                          
[40] "Loading package BEAST v2.6.0"                                                    
[41] "Loading package BEASTLabs v1.9.0"                                                
[42] "Loading package BEAST v2.6.0"                                                    
[43] "Alignment(temp)"                                                                 
[44] "  100 taxa"                                                                      
[45] "  1000 sites"                                                                    
[46] "  1000 patterns"                                                                 
[47] ""                                                                                
[48] "Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path"            
[49] "TreeLikelihood(treeLikelihood.temp0) uses BeerLikelihoodCore4"                   
[50] "  Alignment(temp): [taxa, patterns, sites] = [100, 1000, 1000]"                  
[51] "===============================================================================" 
[52] "Citations for this model:"                                                       
[53] ""                                                                                
[54] "Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, "
[55] "  Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled et al. "                
[56] "  BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. " 
[57] "  PLoS computational biology 15, no. 4 (2019): e1006650."                        
[58] ""                                                                                
[59] "===============================================================================" 
[60] "Done!"                                                                           
[1] "cmd: /apps/generic/software/Java/1.8.0_192/jre/bin/java -jar '/home/p230198/.local/share/beast/lib/launcher.jar' -seed 1565709199.47784 -statefile \"/local/tmp/Rtmpf9l8SU/file160fd6f7b1e9b.xml.state\" -overwrite \"/local/tmp/Rtmpf9l8SU/file160fd769ab7b2.xml\""
Error in beastier::run_beast2(input_filename = beast2_input_filename,  : 
  BEAST2 .log file not created at '/home/p230198/GitHubs/beastier/scripts/temp.log' 
Maybe no permission to write at that location?
Calls: <Anonymous> -> <Anonymous> -> bbt_run -> <Anonymous>
In addition: Warning message:
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/p230198/.local/share/beast/lib/launcher.jar' -seed 1565709199.47784 -statefile "/local/tmp/Rtmpf9l8SU/file160fd6f7b1e9b.xml.state" -overwrite "/local/tmp/Rtmpf9l8SU/file160fd769ab7b2.xml" 2>&1' had status 1
Execution halted

###############################################################################
Peregrine Cluster
Job 7287202 for user 'p230198'
Finished at: Tue Aug 13 17:13:39 CEST 2019

Job details:
============

Name                : run_r_script
User                : p230198
Partition           : regular
Nodes               : pg-node032
Cores               : 1
State               : FAILED
Submit              : 2019-08-13T17:11:24
Start               : 2019-08-13T17:11:25
End                 : 2019-08-13T17:13:39
Reserved walltime   : 01:00:00
Used walltime       : 00:02:14
Used CPU time       : 00:01:27 (efficiency: 65.06%)
% User (Computation): 86.34%
% System (I/O)      : 13.66%
Mem reserved        : 1G/node
Max Mem used        : 442.35M (pg-node032)
Max Disk Write      : 286.72K (pg-node032)
Max Disk Read       : 9.52M (pg-node032)

Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

################################################################################
richelbilderbeek commented 5 years ago

Note that the program runs fine the first time. It runs into trouble the second time, when overwriting some temp files! To fix this, I will in good conscious delete those naughty temp files.

richelbilderbeek commented 5 years ago

Running it locally, an error is exposed:

richel@sonic:~$ '/usr/lib/jvm/java-11-openjdk-amd64/bin/java' -jar '/home/richel/.local/share/beast/lib/launcher.jar' -seed 1565710179.23933 -statefile "/home/richel/.cache/file75953f83798e/file75954b8041c.xml.state" -overwrite "/home/richel/.cache/file759532c6287f/file7595385eaa7e.xml" 2>&1

Argument, -seed has a bad integer value: 1565710179.23933

rng_seed must be a whole number.

richelbilderbeek commented 5 years ago

Bug is caused by infer_phylogeny, that uses the Sys.Time:

  if (is.null(mcmc_seed)) 
    mcmc_seed = as.numeric(Sys.time())
  intended_options <- beastier::create_beast2_options(overwrite = TRUE, 
    beast2_working_dir = getwd(), output_trees_filenames = paste0(treatment_name, 
      ".trees"), output_log_filename = paste0(treatment_name, 
      ".log"), rng_seed = mcmc_seed, verbose = TRUE)
richelbilderbeek commented 5 years ago

Solved :+1: