Error when running PC alg (some CSV file)

[ArnoVel]

Hi,
As you know, I have installed most of the packages and attempted to run PC alg on sachs as well as fsgnn.
I thought I was out of trouble as the R setup looked fine, but when calling the following python3.6 snippet

from cdt.causality.graph.PC import PC

pc = PC(CItest="hsic",method_indep="rcit")
pcgraph = pc.predict(data)

The interpreter spat out the following error message:

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source()

FileNotFoundError: [Errno 2] File b'/tmp/cdt_pc_0f4d2452-ff3c-4a84-81dd-73ab5b4d474b//result.csv' does not exist: b'/tmp/cdt_pc_0f4d2452-ff3c-4a84-81dd-73ab5b4d474b//result.csv'

Any idea of what this is about?

Regards,
A.V

NB: here is the full error printout

--------------------------------------------------------------------
FileNotFoundError                  Traceback (most recent call last)
<ipython-input-50-db1fca6dbddc> in <module>
----> 1 pcgraph = pc.predict(data)

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/model.py in predict(self, df_data, graph, **kwargs)
     61         """
     62         if graph is None:
---> 63             return self.create_graph_from_data(df_data, **kwargs)
     64         elif isinstance(graph, nx.DiGraph):
     65             return self.orient_directed_graph(df_data, graph, **kwargs)

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/PC.py in create_graph_from_data(self, data, **kwargs)
    257         self.arguments['{VERBOSE}'] = str(self.verbose).upper()
    258 
--> 259         results = self._run_pc(data, verbose=self.verbose)
    260 
    261         return nx.relabel_nodes(nx.DiGraph(results),

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/PC.py in _run_pc(self, data, fixedEdges, fixedGaps, verbose)
    300         except Exception as e:
    301             rmtree(run_dir)
--> 302             raise e
    303         except KeyboardInterrupt:
    304             rmtree(run_dir)

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/PC.py in _run_pc(self, data, fixedEdges, fixedGaps, verbose)
    296 
    297             pc_result = launch_R_script("{}/R_templates/pc.R".format(os.path.dirname(os.path.realpath(__file__))),
--> 298                                         self.arguments, output_function=retrieve_result, verbose=verbose)
    299         # Cleanup
    300         except Exception as e:

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/utils/R.py in launch_R_script(template, arguments, output_function, verbose, debug)
    198         if not debug:
    199             rmtree(base_dir)
--> 200         raise e
    201     except KeyboardInterrupt:
    202         if not debug:

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/utils/R.py in launch_R_script(template, arguments, output_function, verbose, debug)
    192                                            stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
    193             process.wait()
--> 194             output = output_function()
    195 
    196     # Cleaning up

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/cdt/causality/graph/PC.py in retrieve_result()
    284 
    285         def retrieve_result():
--> 286             return read_csv('{}/result.csv'.format(run_dir), delimiter=',').values
    287 
    288         try:

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
    683         )
    684 
--> 685         return _read(filepath_or_buffer, kwds)
    686 
    687     parser_f.__name__ = name

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds)
    455 
    456     # Create the parser.
--> 457     parser = TextFileReader(fp_or_buf, **kwds)
    458 
    459     if chunksize or iterator:

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in __init__(self, f, engine, **kwds)
    893             self.options["has_index_names"] = kwds["has_index_names"]
    894 
--> 895         self._make_engine(self.engine)
    896 
    897     def close(self):

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in _make_engine(self, engine)
   1133     def _make_engine(self, engine="c"):
   1134         if engine == "c":
-> 1135             self._engine = CParserWrapper(self.f, **self.options)
   1136         else:
   1137             if engine == "python":

~/progtools/python/virtualenvs/tfcuda/lib/python3.6/site-packages/pandas/io/parsers.py in __init__(self, src, **kwds)
   1915         kwds["usecols"] = self.usecols
   1916 
-> 1917         self._reader = parsers.TextReader(src, **kwds)
   1918         self.unnamed_cols = self._reader.unnamed_cols
   1919 

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader.__cinit__()

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source()

FileNotFoundError: [Errno 2] File b'/tmp/cdt_pc_0f4d2452-ff3c-4a84-81dd-73ab5b4d474b//result.csv' does not exist: b'/tmp/cdt_pc_0f4d2452-ff3c-4a84-81dd-73ab5b4d474b//result.csv'

[ArnoVel]

If my understanding is correct, either pc.R does not write results (because it fails to do so, or is simply not called) ; or PC.py does not know how/where to get the results back.

More detailed:

• Check the fact R package can load

dfpkg = DefaultRPackages()
dfpkg.check_R_package('some_package')

Returns True for all the packages needed.

• The scripts seem to be writing to funny paths such as /tmp/cdt_pc_ea47a7a6-85c3-4624-a8a8-144b68ae72b0//data.csv. Wouldn't the double-slash ( <something>//<something>) mess things up?
• The problem seems to come from the launch_R_script function from R.py

[ArnoVel]

Update: problem comes from the R script pc.R.
The following pops on the terminal when the process is called:

Loading required package: momentchi2
Loading required package: MASS
Casting arguments...
Error in skeleton(suffStat, indepTest, alpha, labels = labels, method = skel.method,  : 
  Evaluation error: object 'pval' not found.
Calls: runPC -> <Anonymous> -> skeleton
Execution halted

Investigating further...

[ArnoVel]

Strangely enough, the CRAN pcalg doc doesn't list any pval variable for the skeleton function..
Edit: this is what I found through R's getAnywhere() : the relevant bit of the skeleton function is:

                  if (length_nbrs >= ord) {
                    if (length_nbrs > ord) 
                      done <- FALSE
                    S <- seq_len(ord)
                    repeat {
                      n.edgetests[ord1] <- n.edgetests[ord1] + 
                        1
                      pval <- indepTest(x, y, nbrs[S], suffStat)
                      if (verbose) 
                        cat("x=", x, " y=", y, " S=", nbrs[S], 
                          ": pval =", pval, "\n")
                      if (is.na(pval)) 
                        pval <- as.numeric(NAdelete)
                      if (pMax[x, y] < pval) 
                        pMax[x, y] <- pval
                      if (pval >= alpha) {
                        G[x, y] <- G[y, x] <- FALSE
                        sepset[[x]][[y]] <- nbrs[S]
                        break
                      }
                      else {
                        nextSet <- getNextSet(length_nbrs, ord, 
                          S)
                        if (nextSet$wasLast) 
                          break
                        S <- nextSet$nextSet
                      }

What do you think? Some problem related to the IndepTest itself, or the way it is passed to R

[ArnoVel]

Ok, went to check the pc.R file, and something bugs me.
First, you define the PC options this way

# additional options for PC
  optionsList <- list("indepTest"={CITEST}, "fixedEdges"=fixedEdges,
                      "NAdelete"=TRUE, "m.max"=Inf, "u2pd" = "relaxed",
                      "skel.method"= "stable.fast", "conservative"=FALSE,
                      "maj.rule"=TRUE, "solve.confl"=FALSE, numCores={NJOBS})

which becomes (after your template editing) in my case

  # additional options for PC
  optionsList <- list("indepTest"=kpcalg::kernelCItest, "fixedEdges"=fixedEdges,
                      "NAdelete"=TRUE, "m.max"=Inf, "u2pd" = "relaxed",
                      "skel.method"= "stable.fast", "conservative"=FALSE,
                      "maj.rule"=TRUE, "solve.confl"=FALSE, numCores=1)

But then, both in the template pc.R and after-editing, I find that the last function call

result <- runPC(dataset, suffStat = NULL, parentsOf, alpha,
               variableSelMat, setOptions,
               directed, verbose, fixedEdges, fixedGaps, CI_test)

is made using some variable CI_test which I cannot find in any of the two files?

Would that be the problem ? (as you know that pval , the output of indepTest is the root of my issue)

Any clue would help me greatly!

Edit: So far, the variable CI_test takes the place of result in the function call, which is immediately set to an empty list through

result <- vector("list", length = length(parentsOf))

I do not see the point of this? And why give result as function argument; and why give CI_test such a suggestive name ? Much confusion

[diviyank]

Hi,
Thanks for the detailed bug report, I'll look into this
The strange point is that the Continuous integration tool did not report any bug....

Best,
Diviyan

[braden-scherting]

Hi All,

I'll just note that I encounter this error for all R-dependent cdt.causality.graph methods. The problem persists with custom data.

Running the basic tutorial code verbatim:

PC is ran on the skeleton of the given graph.
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
 in 
----> 1 model.predict(data, new_skeleton)

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/cdt/causality/graph/model.py in predict(self, df_data, graph, **kwargs)
     63             return self.create_graph_from_data(df_data, **kwargs)
     64         elif isinstance(graph, nx.DiGraph):
---> 65             return self.orient_directed_graph(df_data, graph, **kwargs)
     66         elif isinstance(graph, nx.Graph):
     67             return self.orient_undirected_graph(df_data, graph, **kwargs)

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/cdt/causality/graph/PC.py in orient_directed_graph(self, data, graph, *args, **kwargs)
    240         """
    241         warnings.warn("PC is ran on the skeleton of the given graph.")
--> 242         return self.orient_undirected_graph(data, nx.Graph(graph), *args, **kwargs)
    243 
    244     def create_graph_from_data(self, data, **kwargs):

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/cdt/causality/graph/PC.py in orient_undirected_graph(self, data, graph, **kwargs)
    219         fg = DataFrame(1 - fe.values)
    220 
--> 221         results = self._run_pc(data, fixedEdges=fe, fixedGaps=fg, verbose=self.verbose)
    222 
    223         return nx.relabel_nodes(nx.DiGraph(results),

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/cdt/causality/graph/PC.py in _run_pc(self, data, fixedEdges, fixedGaps, verbose)
    302         except Exception as e:
    303             rmtree(run_dir)
--> 304             raise e
    305         except KeyboardInterrupt:
    306             rmtree(run_dir)

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/cdt/causality/graph/PC.py in _run_pc(self, data, fixedEdges, fixedGaps, verbose)
    298 
    299             pc_result = launch_R_script("{}/R_templates/pc.R".format(os.path.dirname(os.path.realpath(__file__))),
--> 300                                         self.arguments, output_function=retrieve_result, verbose=verbose)
    301         # Cleanup
    302         except Exception as e:

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/cdt/utils/R.py in launch_R_script(template, arguments, output_function, verbose, debug)
    198         if not debug:
    199             rmtree(base_dir)
--> 200         raise e
    201     except KeyboardInterrupt:
    202         if not debug:

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/cdt/utils/R.py in launch_R_script(template, arguments, output_function, verbose, debug)
    192                                            stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
    193             process.wait()
--> 194             output = output_function()
    195 
    196     # Cleaning up

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/cdt/causality/graph/PC.py in retrieve_result()
    286 
    287         def retrieve_result():
--> 288             return read_csv('{}/result.csv'.format(run_dir), delimiter=',').values
    289 
    290         try:

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/pandas/io/parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
    683         )
    684 
--> 685         return _read(filepath_or_buffer, kwds)
    686 
    687     parser_f.__name__ = name

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds)
    455 
    456     # Create the parser.
--> 457     parser = TextFileReader(fp_or_buf, **kwds)
    458 
    459     if chunksize or iterator:

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/pandas/io/parsers.py in __init__(self, f, engine, **kwds)
    893             self.options["has_index_names"] = kwds["has_index_names"]
    894 
--> 895         self._make_engine(self.engine)
    896 
    897     def close(self):

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/pandas/io/parsers.py in _make_engine(self, engine)
   1133     def _make_engine(self, engine="c"):
   1134         if engine == "c":
-> 1135             self._engine = CParserWrapper(self.f, **self.options)
   1136         else:
   1137             if engine == "python":

~/.pyenv/versions/3.7.3/envs/cause_env/lib/python3.7/site-packages/pandas/io/parsers.py in __init__(self, src, **kwds)
   1915         kwds["usecols"] = self.usecols
   1916 
-> 1917         self._reader = parsers.TextReader(src, **kwds)
   1918         self.unnamed_cols = self._reader.unnamed_cols
   1919 

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader.__cinit__()

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source()

FileNotFoundError: [Errno 2] File b'/var/folders/r0/l_20fjfn6vs6l848f3jfysj00000gn/T/cdt_pc_b91480ab-9011-49ca-8f51-0f3aa9c5d861//result.csv' does not exist: b'/var/folders/r0/l_20fjfn6vs6l848f3jfysj00000gn/T/cdt_pc_b91480ab-9011-49ca-8f51-0f3aa9c5d861//result.csv'

[diviyank]

Sorry for the delay.
To solve @ArnoVel 's issue, it originates from :

pc = PC(CItest="hsic",method_indep="rcit")

These two options are incompatible. to use RCIT, you should use CItest='randomized'.
I should change the API to make it simpler to avoid these issues.

[diviyank]

@nedarb708 , I think your issue is different; could you explain your setup ? Please provide the lines that error. This FilenotFoundError originates from the R process that errors. Are you running it in a docker ?

[ArnoVel]

@Diviyan-Kalainathan Thanks for this, it makes sense !
I do think however my intuition of first picking the type of test, and then specifying that I wanted to use the randomized version to approximate the HSIC test makes sense in terms of design?
Anyways, thank you for the explanation :)

[diviyank]

It should be much easier to understand, and errors might be avoided in the future :)