Update fails with "supervisorctl: command not found"

2.4.2 was working happily in Cluster mode (1 master, 6 workers) installed on CentOS 7.
Trying to update to 2.4.5 yesterday encountered exactly the same error - rolled-back to a backup and tried again today with 2.4.6 - here is the output:

[cryosparc@norfolk ~]$ cryosparcm update --check
CryoSPARC current version v2.4.2
          update starting on Fri 30 Nov 10:24:02 UTC 2018

  current version v2.4.2
      new version v2.4.6

Update available!
[cryosparc@norfolk ~]$ cryosparcm update
CryoSPARC current version v2.4.2
          update starting on Fri 30 Nov 10:24:06 UTC 2018

No version specified - updating to latest version.

=============================
Updating to version v2.4.6.
=============================
CryoSPARC is running.
Stopping cryosparc.
command_proxy: stopped
command_vis: stopped
webapp: stopped
command_core: stopped
database: stopped
Shut down
  Downloading master update...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
100  653M  100  653M    0     0  1443k      0  0:07:43  0:07:43 --:--:-- 1450k
  Downloading worker update...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  721M  100  721M    0     0  1462k      0  0:08:25  0:08:25 --:--:-- 1464k
  Done.

 Update will now be applied to the master installation, 
 followed by worker installations on other node.

  Deleting old files...
  Extracting...
  Done.
  Updating dependencies...
Checking dependencies... 
Dependencies for python have changed - reinstalling...
------------------------------------------------------------------------
rm: cannot remove ‘/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib’: Directory not empty
  Installing anaconda python...
------------------------------------------------------------------------
ERROR: File or directory already exists: '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda'
If you want to update an existing installation, use the -u option.
------------------------------------------------------------------------
 Done.
 anaconda python installation successful.
------------------------------------------------------------------------
 Preparing to install all conda packages...
------------------------------------------------------------------------
/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 14: conda: command not found
------------------------------------------------------------------------
 Done.
 conda packages installation successful.
------------------------------------------------------------------------
 Preparing to install all pip packages...
------------------------------------------------------------------------
/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps_bundle_hashes/python/install_python.sh: line 21: pip: command not found
------------------------------------------------------------------------
 Done.
 pip packages installation successful.
------------------------------------------------------------------------
 Main dependency installation completed. Continuing...
------------------------------------------------------------------------
Completed.
Currently checking hash for mongodb
Dependencies for mongodb have not changed.
Completed dependency check. 
 
Successfully updated master from version v2.4.2 to version v2.4.6.
 
Starting cryoSPARC System master process..
/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/bin/cryosparcm: line 369: supervisorctl: command not found

Is there any way to force the dependency installer to run separately?

Here is my attempt:

[cryosparc@norfolk cryosparc2_master]$ cryosparcm deps
ERROR: ld.so: object '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0' from LD_PRELOAD cannot be preloaded: ignored.
ERROR: ld.so: object '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0' from LD_PRELOAD cannot be preloaded: ignored.
ERROR: ld.so: object '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0' from LD_PRELOAD cannot be preloaded: ignored.
ERROR: ld.so: object '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0' from LD_PRELOAD cannot be preloaded: ignored.
ERROR: ld.so: object '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0' from LD_PRELOAD cannot be preloaded: ignored.
ERROR: ld.so: object '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0' from LD_PRELOAD cannot be preloaded: ignored.
ERROR: ld.so: object '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0' from LD_PRELOAD cannot be preloaded: ignored.
ERROR: ld.so: object '/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0' from LD_PRELOAD cannot be preloaded: ignored.
Checking dependencies... 
Dependencies for python have not changed.
Currently checking hash for mongodb
Dependencies for mongodb have not changed.
Completed dependency check.

Okay, I moved the deps_hashes and re-ran cryosparcm deps and it seems to have made a difference - but now the service appears to start but hasn’t actually started the 39000 port

[cryosparc@norfolk ~]$ cryosparcm start
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
  cryosparc command core startup complete.
command_vis: started
command_proxy: started
webapp: started
-----------------------------------------------------

CryoSPARC master started. 
 From this machine, access the webapp at
    http://localhost:39000
 From other machines on the network, access at
    http://norfolk.maas:39000

Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.
[cryosparc@norfolk ~]$ ss -tln
State       Recv-Q Send-Q                                 Local Address:Port                                                Peer Address:Port              
LISTEN      0      128                                                *:39003                                                          *:*                  
LISTEN      0      50                                                 *:39004                                                          *:*                  
LISTEN      0      64                                                 *:33440                                                          *:*                  
LISTEN      0      128                                                *:6818                                                           *:*                  
LISTEN      0      5                                                  *:8649                                                           *:*                  
LISTEN      0      64                                                 *:37870                                                          *:*                  
LISTEN      0      128                                                *:111                                                            *:*                  
LISTEN      0      128                                                *:50641                                                          *:*                  
LISTEN      0      128                                                *:22                                                             *:*                  
LISTEN      0      128                                        127.0.0.1:631                                                            *:*                  
LISTEN      0      128                                                *:39001                                                          *:*                  
LISTEN      0      128                                                *:39002                                                          *:*                  
LISTEN      0      128                                        127.0.0.1:6010                                                           *:*                  
LISTEN      0      64                                                :::6556                                                          :::*                  
LISTEN      0      64                                                :::38595                                                         :::*                  
LISTEN      0      128                                               :::58187                                                         :::*                  
LISTEN      0      128                                               :::111                                                           :::*                  
LISTEN      0      128                                               :::22                                                            :::*                  
LISTEN      0      128                                              ::1:631                                                           :::*                  
LISTEN      0      64                                                :::46841                                                         :::*                  
LISTEN      0      128                                              ::1:6010                                                          :::*                  
[cryosparc@norfolk ~]$

Re-installing the dependencies:

[cryosparc@norfolk cryosparc2_master]$ mv deps_hashes deps_hashes.old
[cryosparc@norfolk cryosparc2_master]$ cryosparcm deps
Checking dependencies... 
Dependencies for python have changed - reinstalling...
------------------------------------------------------------------------
  Installing anaconda python...
------------------------------------------------------------------------
PREFIX=/net/zeta/usr/mbu/software/cryosparc2/cryosparc2_master/deps/anaconda
installing: python-2.7.14-h1571d57_29 ...
Python 2.7.14 :: Anaconda, Inc.
installing: ca-certificates-2017.08.26-h1d4fec5_0 ...
installing: conda-env-2.6.0-h36134e3_1 ...
installing: libgcc-ng-7.2.0-h7cc24e2_2 ...
installing: libstdcxx-ng-7.2.0-h7a57d05_2 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: ncurses-6.0-h9df7e31_2 ...
installing: openssl-1.0.2n-hb7f436b_0 ...
installing: tk-8.6.7-hc745277_3 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-ha838bed_2 ...
installing: libedit-3.1-heed3624_0 ...
installing: readline-7.0-ha6073c6_4 ...
installing: sqlite-3.20.1-hb898158_2 ...
installing: asn1crypto-0.23.0-py27h7b0c810_0 ...
installing: certifi-2017.11.5-py27h71e7faf_0 ...
installing: chardet-3.0.4-py27hfa10054_1 ...
installing: enum34-1.1.6-py27h99a27e9_1 ...
installing: idna-2.6-py27h5722d68_1 ...
installing: ipaddress-1.0.18-py27h337fd85_0 ...
installing: pycosat-0.6.3-py27ha4109ae_0 ...
installing: pycparser-2.18-py27hefa08c5_1 ...
installing: pysocks-1.6.7-py27he2db6d2_1 ...
installing: ruamel_yaml-0.11.14-py27h672d447_2 ...
installing: six-1.11.0-py27h5f960f1_1 ...
installing: cffi-1.11.2-py27ha7929c6_0 ...
installing: setuptools-36.5.0-py27h68b189e_0 ...
installing: cryptography-2.1.4-py27h6697b16_0 ...
installing: wheel-0.30.0-py27h2bc6bb2_1 ...
installing: pip-9.0.1-py27ha730c48_4 ...
installing: pyopenssl-17.5.0-py27hcee3be0_0 ...
installing: urllib3-1.22-py27ha55213b_0 ...
installing: requests-2.18.4-py27hc5b0589_1 ...
installing: conda-4.3.31-py27_0 ...
installation finished.
------------------------------------------------------------------------
 Done.
 anaconda python installation successful.
------------------------------------------------------------------------
 Preparing to install all conda packages...
------------------------------------------------------------------------
------------------------------------------------------------------------
 Done.
 conda packages installation successful.
------------------------------------------------------------------------
 Preparing to install all pip packages...
------------------------------------------------------------------------
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-JSONRPC-0.3.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-PyMongo-0.5.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/libtiff-0.4.2.tar.gz
Requirement already satisfied: Flask>=0.10 in ./deps/anaconda/lib/python2.7/site-packages (from Flask-JSONRPC==0.3.1)
Requirement already satisfied: PyMongo>=2.5 in ./deps/anaconda/lib/python2.7/site-packages (from Flask-PyMongo==0.5.1)
Requirement already satisfied: Werkzeug>=0.7 in ./deps/anaconda/lib/python2.7/site-packages (from Flask>=0.10->Flask-JSONRPC==0.3.1)
Requirement already satisfied: Jinja2>=2.4 in ./deps/anaconda/lib/python2.7/site-packages (from Flask>=0.10->Flask-JSONRPC==0.3.1)
Requirement already satisfied: itsdangerous>=0.21 in ./deps/anaconda/lib/python2.7/site-packages (from Flask>=0.10->Flask-JSONRPC==0.3.1)
Requirement already satisfied: click>=2.0 in ./deps/anaconda/lib/python2.7/site-packages (from Flask>=0.10->Flask-JSONRPC==0.3.1)
Requirement already satisfied: MarkupSafe in ./deps/anaconda/lib/python2.7/site-packages (from Jinja2>=2.4->Flask>=0.10->Flask-JSONRPC==0.3.1)
Skipping bdist_wheel for Flask-JSONRPC, due to binaries being disabled for it.
Skipping bdist_wheel for Flask-PyMongo, due to binaries being disabled for it.
Skipping bdist_wheel for libtiff, due to binaries being disabled for it.
Installing collected packages: Flask-JSONRPC, Flask-PyMongo, libtiff
  Running setup.py install for Flask-JSONRPC ... done
  Running setup.py install for Flask-PyMongo ... done
  Running setup.py install for libtiff ... done
Successfully installed Flask-JSONRPC-0.3.1 Flask-PyMongo-0.5.1 libtiff-0.4.2
You are using pip version 9.0.1, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
------------------------------------------------------------------------
 Done.
 pip packages installation successful.
------------------------------------------------------------------------
 Main dependency installation completed. Continuing...
------------------------------------------------------------------------
Completed.
Currently checking hash for mongodb
Dependencies for mongodb have changed - reinstalling...
------------------------------------------------------------------------
mongodb 3.4.10 installation successful.
------------------------------------------------------------------------
Completed.
Completed dependency check.

“cryosparcm log webapp” shows nothing logged since 28th, which is when it was last successfully used.

For this part of problem; re-installing dependencies after removing them manually seems to have solved something.
I’ve made a separate post regarding the non-starting of port 39000