Not all conformance tests pass with udocker

---

## Expected Behavior
Conformance tests should all pass

## Actual Behavior
3 fail

## Workflow Code
```
./run_test.sh EXTRA=--user-space-docker-cmd=/home/ubuntu/udocker
```

## Full Traceback
```pytb
--- Running conformance test v1.0 on /home/ubuntu/.local/bin/cwl-runner ---
/home/ubuntu/.local/bin/cwl-runner 1.0.20180525185854
Test [1/131] General test of command line generation
Test [2/131] Test nested prefixes with arrays
Test [3/131] Test nested command line bindings
Test [4/131] Test command line with optional input (missing)
Test [5/131] Test command line with optional input (provided)
Test [6/131] Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature
Test [7/131] Test command execution in Docker with stdout redirection
Test [8/131] Test command execution in Docker with simplified syntax stdout redirection
Test [9/131] Test command execution in Docker with stdout redirection
Test [10/131] Test command line with stderr redirection
Test [11/131] Test command line with stderr redirection, brief syntax
Test [12/131] Test command line with stderr redirection, named brief syntax
Test [13/131] Test command execution in Docker with stdin and stdout redirection
Test [14/131] Test default usage of Any in expressions.
Test [15/131] Test explicitly passing null to Any type inputs with default values.
Test [16/131] Testing the string 'null' does not trip up an Any with a default value.
Test [17/131] Test Any without defaults can be unspecified.
Test [18/131] Test explicitly passing null to Any type without a default value.
Test [19/131] Testing the string 'null' does not trip up an Any without a default value.
Test [20/131] Testing Any type compatibility in outputSource
Test [21/131] Test command execution in with stdin and stdout redirection
Test [22/131] Test ExpressionTool with Docker-based expression engine
Test [23/131] Test outputEval to transform output
Test [24/131] Test two step workflow with imported tools
Test [25/131] Test two step workflow with inline tools
Test [26/131] Test single step workflow with Scatter step
Test [27/131] Test single step workflow with Scatter step and two data links connected to
same input, default merge behavior

Test [28/131] Test single step workflow with Scatter step and two data links connected to
same input, nested merge behavior

Test [29/131] Test single step workflow with Scatter step and two data links connected to
same input, flattened merge behavior

Test [30/131] Test that no MultipleInputFeatureRequirement is necessary when
workflow step source is a single-item list

Test [31/131] Test workflow with default value for input parameter (missing)
Test [32/131] Test workflow with default value for input parameter (provided)
Test [33/131] Test that workflow defaults override tool defaults
Test [34/131] Test EnvVarRequirement
Test [35/131] Test workflow scatter with single scatter parameter
Test [36/131] Test workflow scatter with two scatter parameters and nested_crossproduct join method
Test [37/131] Test workflow scatter with two scatter parameters and flat_crossproduct join method
Test [38/131] Test workflow scatter with two scatter parameters and dotproduct join method
Test [39/131] Test workflow scatter with single empty list parameter
Test [40/131] Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty
Test [41/131] Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty
Test [42/131] Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method
Test [43/131] Test workflow scatter with two empty scatter parameters and dotproduct join method
Test [44/131] Test Any type input parameter
Test [45/131] Test nested workflow
Test [46/131] Test requirement priority
Test [47/131] Test requirements override hints
Test [48/131] Test requirements on workflow steps
Test [49/131] Test default value on step input parameter
Test [50/131] Test use default value on step input parameter with empty source
Test [51/131] Test use default value on step input parameter with null source
Test [52/131] Test default value on step input parameter overridden by provided source
Test [53/131] Test simple workflow
Test [54/131] Test unknown hints are ignored.
Test [55/131] Test InitialWorkDirRequirement linking input files and capturing secondaryFiles
on input and output. Also tests the use of a variety of parameter references
and expressions in the secondaryFiles field.

Test [56/131] Test InitialWorkDirRequirement with expression in filename.

Test [57/131] Test if trailing newline is present in file entry in InitialWorkDir
Test [58/131] Test inline expressions

Test [59/131] Test SchemaDefRequirement definition used in tool parameter

Test [60/131] Test SchemaDefRequirement definition used in workflow parameter

Test [61/131] Test parameter evaluation, no support for JS expressions

Test [62/131] Test parameter evaluation, with support for JS expressions

Test [63/131] Test metadata
Test [64/131] Test simple format checking.

Test [65/131] Test format checking against ontology using subclassOf.

Test [66/131] Test format checking against ontology using equivalentClass.

Test [67/131] Test optional output file and optional secondaryFile on output.

Test [68/131] Test that second expression in concatenated valueFrom is not ignored
Test [69/131] Test valueFrom on workflow step.
Test [70/131] Test valueFrom on workflow step with multiple sources
Test [71/131] Test valueFrom on workflow step referencing other inputs
Test [72/131] Test record type output binding.
Test [73/131] Test support for reading cwl.output.json when running in a Docker container
and just 'path' is provided.

Test failed: /home/ubuntu/.local/bin/cwl-runner --user-space-docker-cmd=/home/ubuntu/udocker --outdir=/tmp/tmpG1CCYH --quiet v1.0/test-cwl-out.cwl v1.0/empty.json
Test support for reading cwl.output.json when running in a Docker container
and just 'path' is provided.

Returned non-zero

******************************************************************************
* *
* STARTING e743cc2b-4a84-3645-b0af-958b50f3035b *
* *
******************************************************************************
executing: sh
Exception while running job
Traceback (most recent call last):
File "/home/ubuntu/.local/lib/python2.7/site-packages/cwltool/job.py", line 267, in _execute
outputs = self.collect_outputs(self.outdir)
File "/home/ubuntu/.local/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 550, in collect_output_ports
ret = json.load(f)
File "/usr/lib/python2.7/json/__init__.py", line 291, in load
**kw)
File "/usr/lib/python2.7/json/__init__.py", line 339, in loads
return _default_decoder.decode(s)
File "/usr/lib/python2.7/json/decoder.py", line 364, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python2.7/json/decoder.py", line 380, in raw_decode
obj, end = self.scan_once(s, idx)
ValueError: Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
[job test-cwl-out.cwl] completed permanentFail
Final process status is permanentFail

Test [74/131] Test support for reading cwl.output.json when running in a Docker container
and just 'location' is provided.

Test failed: /home/ubuntu/.local/bin/cwl-runner --user-space-docker-cmd=/home/ubuntu/udocker --outdir=/tmp/tmpSCzsWi --quiet v1.0/test-cwl-out2.cwl v1.0/empty.json
Test support for reading cwl.output.json when running in a Docker container
and just 'location' is provided.

Returned non-zero

******************************************************************************
* *
* STARTING c29df17f-5b82-30be-93f0-42c43e0bcdbb *
* *
******************************************************************************
executing: sh
Exception while running job
Traceback (most recent call last):
File "/home/ubuntu/.local/lib/python2.7/site-packages/cwltool/job.py", line 267, in _execute
outputs = self.collect_outputs(self.outdir)
File "/home/ubuntu/.local/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 550, in collect_output_ports
ret = json.load(f)
File "/usr/lib/python2.7/json/__init__.py", line 291, in load
**kw)
File "/usr/lib/python2.7/json/__init__.py", line 339, in loads
return _default_decoder.decode(s)
File "/usr/lib/python2.7/json/decoder.py", line 364, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python2.7/json/decoder.py", line 380, in raw_decode
obj, end = self.scan_once(s, idx)
ValueError: Expecting property name enclosed in double quotes: line 1 column 2 (char 1)
[job test-cwl-out2.cwl] completed permanentFail
Final process status is permanentFail

Test [75/131] Test support for returning multiple glob patterns from expression
Test [76/131] Test workflow scatter with single scatter parameter and valueFrom on step input
Test [77/131] Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input
Test [78/131] Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input
Test [79/131] Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input
Test [80/131] Test workflow scatter with single scatter parameter and valueFrom on step input
Test [81/131] Test valueFrom eval on scattered input parameter
Test [82/131] Test workflow two input files with same name.
Test [83/131] Test directory input with parameter reference
Test [84/131] Test directory input in Docker
Test [85/131] Test directory output
Test [86/131] Test directories in secondaryFiles
Test [87/131] Test dynamic initial work dir
Test [88/131] Test writable staged files.
Test [89/131] Test file literal as input
Test [90/131] Test expression in InitialWorkDir listing
Test [91/131] Test nameroot/nameext expression in arguments, stdout
Test [92/131] Test directory input with inputBinding
Test [93/131] Test command line generation of array-of-arrays
Test [94/131] Test $HOME and $TMPDIR are set correctly
Test [95/131] Test $HOME and $TMPDIR are set correctly in Docker
Test failed: /home/ubuntu/.local/bin/cwl-runner --user-space-docker-cmd=/home/ubuntu/udocker --outdir=/tmp/tmpCnK5Yr --quiet v1.0/envvar2.cwl v1.0/empty.json
Test $HOME and $TMPDIR are set correctly in Docker
Returned non-zero

******************************************************************************
* *
* STARTING 70b18688-513f-3c81-856e-968005381a50 *
* *
******************************************************************************
executing: sh
HOME= TMPDIR=
/bin/sh: 1: test: =: unexpected operator
[job envvar2.cwl] completed permanentFail
Final process status is permanentFail

Test [96/131] Test that expressionLib requirement of individual tool step overrides expressionLib of workflow.
Test [97/131] Test output of InitialWorkDir
Test [98/131] Test embedded subworkflow
Test [99/131] Test secondaryFiles on array of files.
Test [100/131] Test directory literal output created by ExpressionTool
Test [101/131] Test file literal output created by ExpressionTool
Test [102/131] Test dockerOutputDirectory
Test [103/131] Test hints with $import
Test [104/131] Test warning instead of error when default path is not found
Test [105/131] Test InlineJavascriptRequirement with multiple expressions in the same tool
Test [106/131] Test if a writable input directory is recursivly copied and writable
Test [107/131] Test that missing parameters are null (not undefined) in expression
Test [108/131] Test that provided parameter is not null in expression
Test [109/131] Test compound workflow document
Test [110/131] Test that nameroot and nameext are generated from basename at execution time by the runner
Test [111/131] Test that file path in $(inputs) for initialworkdir is in $(outdir).
Test [112/131] Test single step workflow with Scatter step and two data links connected to
same input, flattened merge behavior. Workflow inputs are set as list

Test [113/131] Test step input with multiple sources with multiple types
Test [114/131] Test that shell directives are not interpreted.
Test [115/131] Test that shell directives are quoted.
Test [116/131] Test empty writable dir with InitialWorkDirRequirement
Test [117/131] Test empty writable dir with InitialWorkDirRequirement inside Docker
Test [118/131] Test dynamic resource reqs referencing inputs
Test [119/131] Test file literal as input without Docker
Test [120/131] Test that OutputBinding.glob is sorted as specified by POSIX
Test [121/131] Test InitialWorkDirRequirement with a nested directory structure from another step
Test [122/131] Test that boolean flags do not appear on command line if inputBinding is empty and not null
Test [123/131] Test that expression engine does not fail to evaluate reference to self with unprovided input
Test [124/131] Test successCodes
Test [125/131] Test simple workflow with a dynamic resource requirement
Test [126/131] Test that empty array input does not add anything to command line
Test [127/131] Test that ResourceRequirement on a step level redefines requirement on the workflow level
Test [128/131] Test valueFrom with constant value overriding provided array inputs
Test [129/131] Test dynamic resource reqs referencing the size of Files inside a Directory
Test [130/131] Test that it is not an error to connect a parameter to a workflow
step, even if the parameter doesn't appear in the `run` process
inputs.

Test [131/131] Test that parameters that doesn't appear in the `run` process
inputs are not present in the input object used to run the tool.

128 tests passed, 3 failures, 0 unsupported features

1 tool tests failed
```

## Your Environment
* cwltool version: 1.0.20180525185854

This is on an a base Ubuntu 16 image, modified like:

```
sudo apt-get update
sudo apt-get -y install python-pip
pip install cwltest
pip install cwlref-runner
sudo apt-get -y install nodejs

curl https://raw.githubusercontent.com/indigo-dc/udocker/master/udocker.py > udocker
chmod u+rx ./udocker
./udocker install

git clone https://github.com/common-workflow-language/common-workflow-language.git cwl-spec
cd cwl-spec
```

I don't know if this is actually a udocker problem, since I can't get the conformance tests to pass with real docker without root, or the tests to run at all with root.