Error running the test script

[lpereira89]

Hello,
I installed the software in HCP system and apparently it was successful. However when running the test script I get the following errors:

Running tests for FastRoot ...
E/users/bo1lpg/miniforge3/lib/python3.12/site-packages/treeswift/Tree.py:1492: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/random_trees/100/input.tre' mode='r' encoding='UTF-8'>
  n = n.parent; c = Node(); n.add_child(c); n = c
ResourceWarning: Enable tracemalloc to get the object allocation traceback
E/users/bo1lpg/miniforge3/lib/python3.12/site-packages/treeswift/Node.py:10: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/random_trees/1000/input.tre' mode='r' encoding='UTF-8'>
  def __init__(self, label=None, edge_length=None):
ResourceWarning: Enable tracemalloc to get the object allocation traceback
E/users/bo1lpg/miniforge3/lib/python3.12/site-packages/treeswift/Node.py:10: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/random_trees/500/input.tre' mode='r' encoding='UTF-8'>
  def __init__(self, label=None, edge_length=None):
ResourceWarning: Enable tracemalloc to get the object allocation traceback
E/users/bo1lpg/miniforge3/lib/python3.12/site-packages/treeswift/Tree.py:1492: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/random_trees/5000/input.tre' mode='r' encoding='UTF-8'>
  n = n.parent; c = Node(); n.add_child(c); n = c
ResourceWarning: Enable tracemalloc to get the object allocation traceback
E/users/bo1lpg/miniforge3/lib/python3.12/site-packages/treeswift/Node.py:10: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/true_trees/input1.trees' mode='r' encoding='UTF-8'>
  def __init__(self, label=None, edge_length=None):
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/users/bo1lpg/miniforge3/lib/python3.12/site-packages/treeswift/Node.py:10: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/true_trees/output1.trees' mode='r' encoding='UTF-8'>
  def __init__(self, label=None, edge_length=None):
ResourceWarning: Enable tracemalloc to get the object allocation traceback
E/users/bo1lpg/miniforge3/lib/python3.12/site-packages/treeswift/Tree.py:1484: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/true_trees/input2.trees' mode='r' encoding='UTF-8'>
  c = Node(); n.add_child(c); n = c
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/users/bo1lpg/miniforge3/lib/python3.12/site-packages/treeswift/Tree.py:1484: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/true_trees/output2.trees' mode='r' encoding='UTF-8'>
  c = Node(); n.add_child(c); n = c
ResourceWarning: Enable tracemalloc to get the object allocation traceback
E/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py:103: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/true_trees/input3.trees' mode='r' encoding='UTF-8'>
  branch_lengths[i+1] = sorted([float(l1), float(l2)])
ResourceWarning: Enable tracemalloc to get the object allocation traceback
/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py:103: ResourceWarning: unclosed file <_io.TextIOWrapper name='/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test/RTT/true_trees/output3.trees' mode='r' encoding='UTF-8'>
  branch_lengths[i+1] = sorted([float(l1), float(l2)])
ResourceWarning: Enable tracemalloc to get the object allocation traceback
.....
======================================================================
ERROR: test_RTT_random_tree_100 (fastroot_tests.unit_test_RTT.RTTTestCase.test_RTT_random_tree_100)
Does RTT root a random trees of size 100 properly?
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test_RTT.py", line 228, in test_RTT_random_tree_100
    score_test_100, RTT_test, branches_test = root_trees(path+"/unit_test/RTT/random_trees/100/input.tre", method='RTT',
                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py", line 84, in root_trees
    a_tree.Reroot()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 171, in Reroot
    self.find_root()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 162, in find_root
    self.Topdown_update()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 61, in Topdown_update
    self.tDown_update(node, self.Opt_function)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 87, in tDown_update
    opt_function(child, SST, deltaT, deltaD, SDT, SSD, ST, SD)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 42, in Opt_function
    G = array([[-1.,0.,0.], [0.,0.,-1.], [1.,0.,0.],[0.,1.,-tmin]])
                                                           ^^^^^
TypeError: bad operand type for unary -: 'dict_values'

======================================================================
ERROR: test_RTT_random_tree_1000 (fastroot_tests.unit_test_RTT.RTTTestCase.test_RTT_random_tree_1000)
Does RTT root a random tree of size 1000 properly?
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test_RTT.py", line 280, in test_RTT_random_tree_1000
    score_test_1000, RTT_test, branches_test = root_trees(path+"/unit_test/RTT/random_trees/1000/input.tre", method='RTT',
                                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py", line 84, in root_trees
    a_tree.Reroot()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 171, in Reroot
    self.find_root()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 162, in find_root
    self.Topdown_update()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 61, in Topdown_update
    self.tDown_update(node, self.Opt_function)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 87, in tDown_update
    opt_function(child, SST, deltaT, deltaD, SDT, SSD, ST, SD)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 42, in Opt_function
    G = array([[-1.,0.,0.], [0.,0.,-1.], [1.,0.,0.],[0.,1.,-tmin]])
                                                           ^^^^^
TypeError: bad operand type for unary -: 'dict_values'

======================================================================
ERROR: test_RTT_random_tree_500 (fastroot_tests.unit_test_RTT.RTTTestCase.test_RTT_random_tree_500)
Does RTT root a random trees of size 500 properly?
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test_RTT.py", line 254, in test_RTT_random_tree_500
    score_test_500, RTT_test, branches_test = root_trees(path+"/unit_test/RTT/random_trees/500/input.tre", method='RTT',
                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py", line 84, in root_trees
    a_tree.Reroot()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 171, in Reroot
    self.find_root()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 162, in find_root
    self.Topdown_update()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 61, in Topdown_update
    self.tDown_update(node, self.Opt_function)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 87, in tDown_update
    opt_function(child, SST, deltaT, deltaD, SDT, SSD, ST, SD)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 42, in Opt_function
    G = array([[-1.,0.,0.], [0.,0.,-1.], [1.,0.,0.],[0.,1.,-tmin]])
                                                           ^^^^^
TypeError: bad operand type for unary -: 'dict_values'

======================================================================
ERROR: test_RTT_random_tree_5000 (fastroot_tests.unit_test_RTT.RTTTestCase.test_RTT_random_tree_5000)
Does RTT root a random trees of size 5000 properly?
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test_RTT.py", line 306, in test_RTT_random_tree_5000
    score_test_5000, RTT_test, branches_test = root_trees(path+"/unit_test/RTT/random_trees/5000/input.tre", method='RTT',
                                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py", line 84, in root_trees
    a_tree.Reroot()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 171, in Reroot
    self.find_root()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 162, in find_root
    self.Topdown_update()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 61, in Topdown_update
    self.tDown_update(node, self.Opt_function)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 87, in tDown_update
    opt_function(child, SST, deltaT, deltaD, SDT, SSD, ST, SD)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 42, in Opt_function
    G = array([[-1.,0.,0.], [0.,0.,-1.], [1.,0.,0.],[0.,1.,-tmin]])
                                                           ^^^^^
TypeError: bad operand type for unary -: 'dict_values'

======================================================================
ERROR: test_RTT_true_trees1 (fastroot_tests.unit_test_RTT.RTTTestCase.test_RTT_true_trees1)
Does RTT root true trees 1-10 properly?
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test_RTT.py", line 29, in test_RTT_true_trees1
    score_test, RTT_test, branches_test = root_trees(path+"/unit_test/RTT/true_trees/input1.trees", method='RTT', timeFile=path+"/unit_test/RTT/true_trees/sampling_times.txt")
                                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py", line 84, in root_trees
    a_tree.Reroot()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 171, in Reroot
    self.find_root()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 162, in find_root
    self.Topdown_update()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 61, in Topdown_update
    self.tDown_update(node, self.Opt_function)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 87, in tDown_update
    opt_function(child, SST, deltaT, deltaD, SDT, SSD, ST, SD)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 42, in Opt_function
    G = array([[-1.,0.,0.], [0.,0.,-1.], [1.,0.,0.],[0.,1.,-tmin]])
                                                           ^^^^^
TypeError: bad operand type for unary -: 'dict_values'

======================================================================
ERROR: test_RTT_true_trees2 (fastroot_tests.unit_test_RTT.RTTTestCase.test_RTT_true_trees2)
Does RTT root true trees 11-20 properly?
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test_RTT.py", line 93, in test_RTT_true_trees2
    score_test, RTT_test, branches_test = root_trees(path+"/unit_test/RTT/true_trees/input2.trees", method='RTT', timeFile=path+"/unit_test/RTT/true_trees/sampling_times.txt")
                                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py", line 84, in root_trees
    a_tree.Reroot()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 171, in Reroot
    self.find_root()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 162, in find_root
    self.Topdown_update()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 61, in Topdown_update
    self.tDown_update(node, self.Opt_function)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 87, in tDown_update
    opt_function(child, SST, deltaT, deltaD, SDT, SSD, ST, SD)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 42, in Opt_function
    G = array([[-1.,0.,0.], [0.,0.,-1.], [1.,0.,0.],[0.,1.,-tmin]])
                                                           ^^^^^
TypeError: bad operand type for unary -: 'dict_values'

======================================================================
ERROR: test_RTT_true_trees3 (fastroot_tests.unit_test_RTT.RTTTestCase.test_RTT_true_trees3)
Does RTT root true trees 21-30 properly?
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/unit_test_RTT.py", line 145, in test_RTT_true_trees3
    score_test, RTT_test, branches_test = root_trees(path+"/unit_test/RTT/true_trees/input3.trees", method='RTT', timeFile=path+"/unit_test/RTT/true_trees/sampling_times.txt")
                                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot_tests/utils.py", line 84, in root_trees
    a_tree.Reroot()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 171, in Reroot
    self.find_root()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 162, in find_root
    self.Topdown_update()
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/Tree_extend.py", line 61, in Topdown_update
    self.tDown_update(node, self.Opt_function)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 87, in tDown_update
    opt_function(child, SST, deltaT, deltaD, SDT, SSD, ST, SD)
  File "/mnt/parscratch/users/bo1lpg/NEOF-project/phylobased-LGT/software/MinVar-Rooting/fastroot/RTT.py", line 42, in Opt_function
    G = array([[-1.,0.,0.], [0.,0.,-1.], [1.,0.,0.],[0.,1.,-tmin]])
                                                           ^^^^^
TypeError: bad operand type for unary -: 'dict_values'

----------------------------------------------------------------------
Ran 12 tests in 2.761s

FAILED (errors=7)

[Hiumin]

Hi, I encountered the same issue and finally managed to make it work.

From the error messages and online discussions, it seems the issue stems from this software package being outdated (or rather its dependencies). The article was published quite some time ago, and while FastRoot was still being maintained for a couple of years, the behavior of pip and setuptools had had major changes during that time, along with their concurrent major Python versions. Of course, the syntax and behavior of numpy and cvxopt are also different now.

As such, you would need to install older versions of pip and setuptools and build the corresponding older versions of numpy and cvxopt. Assuming you are using conda/mamba, the following should work (do the installation one step at a time in case problems arise again):

micromamba create -n FastRoot-1.5 -c conda-forge -c bioconda
micromamba activate FastRoot-1.5
micromamba install setuptools==42.0.2
pip install treeswift==1.1.14
pip install numpy==1.19.0
pip install cvxopt==1.2.5
pip install FastRoot==1.5

However, there is still another issue: the end-of-line characters in the scripts are actually CR LF (used by DOS/Windows systems). You can see that with:

head "$(command -v FastRoot.py)" | cat -A

There is a nice tool called dos2unix that can do the conversion back to LF and is probably available on your server as well. You would need to locate all the FastRoot-related executable scripts that were installed into your conda/mamba environment bin and do the conversion on all of them (the command below will act on all the executables that are there).

find $HOME/$USER/.mamba/envs/FastRoot-1.5/bin -type f -exec dos2unix {} \;

If dos2unix is not available, you can try something like sed or tr (such as in here). If you want to install from the source code by cloning the git repo then you will need to do the conversion on the scripts before doing pip install ., but I have not tested that.

Once you have done all that, FastRoot_tests.py should complete successfully.

Hope this help : )