I had same issues few days ago. I went thru scripts and saw some issues 
with  pwiz-msi.
Here is my workaround
cd TPP_5.0.0-src

mkdir -p ./extern/ProteoWizard/pwiz-msi

make pwiz-msi

That will download file VERSION. However the format is not good as it has 
spaces instead of dot)

vi ./extern/ProteoWizard/pwiz-msi/VERSION 


Now you need to change Makefile so that it doesn't download VERSION anymore 
by commenting the following lines:

vi ./extern/ProteoWizard/Makefile

pwiz-msi-version :

#        rm -f $(PWIZ_MSIDIR)/VERSION

#        wget -nv -O $(PWIZ_MSIDIR)/VERSION $(PWIZ_TCMSI)/VERSION\?guest=1

Then you should be good to go

make all

Hope that helps

On Monday, October 17, 2016 at 10:51:36 AM UTC-7, Ali wrote:
> Dear all
> Our cluster administrator is getting the following error on Centos Linux 
> x86_84 when he wants to install TPP v5.0. Does any one know what might be 
> the problem and how can we fix the issue?
> [root@compute-0-000 TPP_5.0.0-src]# make all
> /shared/apps/TPP/TPP_5.0.0-src/extern/ProteoWizard/Makefile:353: warning: 
> overriding commands for target `/shared/apps/TPP/TPP_5.0.0-
> src/build/linux-x86_64'
> common.mk:449: warning: ignoring old commands for target 
> `/shared/apps/TPP/TPP_5.0.0-src/build/linux-x86_64'
> make: *** No rule to make target `/shared/apps/TPP/TPP_5.0.0-
> src/extern/ProteoWizard/pwiz-msi', needed by 
> `/shared/apps/TPP/TPP_5.0.0-src/build/linux-x86_64'.  
> Stop.
> [root@compute-0-000 TPP_5.0.0-src]#
> Some packages did not get downloaded with the source code ...?
> Thank you very much,
> Ali 

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