Hi Tobi,
Maybe you could give the administrator installation for Skyline-daily a try:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/daily/page.view?name=install-administrator-64

It does require administrator privileges to install on the system, and it does not automatically update, but it has proven useful in more heavily managed or shared systems where Microsoft ClickOnce installation lacks desirable attributes. This is a more traditional system-wide installation.

If this helps, then you will also be able to solve this problem for Skyline after we make our next release in the coming weeks.

--Brendan

Dear Brendan,

thx for your suggestion. I will give it a try.

Best,
Tobi

Dear Brendan,

I installed skyline as you suggested. So far all worked fine...but, as soon as I would like to install a tool like MSstats I get an error message saying access to ...\Tools\Temp is denied. I checked my account details. It displays local account and Administrator.

A second question: How do I update to the next skyline-daily release? Is there an administrator installation for the reg. skyline?

Best,
Tobi

I just installed the reg. skyline 3.5 (64) using the administrator installation. Installation runs through without any problems. MSstats installation from the tool store quits because ...\Tools\Temp is not accessible.

What to do???

I switched to another Administrator account that was used for the installation of windows 2012 R2. Now, at least the tool installation starts but none of required R packages can be installed. I went to the R command line and installed all packages manually. Attached is the error message I get.

next problem: I somehow managed to get all of the package installed manually using either crane mirrows or the bioclite script. For MStstas I had to download the zip archive from the MSstats website since, version 3.2.3 was not available either from CRAN nor from bioconductor. According to skyline, MSstats is now fully installed (see 1 screen shot). Now I switched back to my reg. working account (tobias) and guess what: No MSstats. :-( :-( :-(

How can I install tools from tool store in a way they are available to all users?

I'll take a look at this.

The way that we were hoping this would work is, if you were planning on installing external tools in Skyline, you would run Skyline by right-clicking on the Skyline icon and choosing "Run as Administrator". Then, using that Skyline you could install tools, and they would go into c:\Program Files\Skyline\Tools. Then you could exit Skyline.

Later, when a regular user on that computer ran Skyline, they would be able to use the tools that you had installed while running Skyline as Administrator.

It sounds like this isn't working right. I'll test this out.

I am seeing the "The system cannot find the file specified" problem when I try to run Skyline as Administrator and try to install the MSstats external tool.

I am not sure exactly why this is happening. Skyline is looking for the file "SkylineProcessRunner.exe", and it's not finding it when it needs to.

It is possible to work around this problem by adding "C:\Program Files\Skyline" to the PATH before you run Skyline as Administrator.

So, that would be:
1. Windows start button
2. Type "Command Prompt".
3. Right-click on the command prompt and choose "Run as Administrator".
4. In the command prompt window, execute the following two commands:
set PATH=%PATH%;"c:\Program Files\Skyline"
skyline.exe

Then, when Skyline runs, you will be able to use Skyline to install the MSstats external tool.

Hi Nick,

thanks for your quick answer. I added the path as you suggested and tested by installing Prego. That worked fine. Thx for the workaround!

Something more general regarding the tool store:

I also tested to install other tools e.g. SProCop and Quasar and realised that every tool requires a different R version, most of them outdated! I know that these specific dependency are not easy to handle, but the current situation is a bit crazy: For installing three tools I would need to install three different R versions on my system and the required libs. It should be possible for the external developers to test their R code once a major R update is released, to at least assure that later R versions are ok, or would that be to much to ask for? Can I somehow force the installation of these tools or is skyline always checking for the specific R version?

Best,
Tobi

Hi Nick,

I just changed back to my regular working account and Prego is not installed. So, it is def. not working. Something else came to my mind: How do you install the required R libs e.g. for MSstats? My R libPaths look like this:

> .libPaths()
[1] "C:/Users/tobias/Documents/R/win-library/3.2"
[2] "C:/Program Files/R/R-3.2.1/library"

but I guess available to all user are only the once installed in [2]. How is skyline installing libs by default? For my working account MSstats for instance was installed in the private branch:

Packages in library ‘C:/Users/tobias/Documents/R/win-library/3.2’:

affy Methods for Affymetrix Oligonucleotide Arrays
affyio Tools for parsing Affymetrix data files
Biobase Biobase: Base functions for Bioconductor
BiocGenerics S4 generic functions for Bioconductor
BiocInstaller Install/Update Bioconductor and CRAN Packages
BiocParallel Bioconductor facilities for parallel evaluation
chron Chronological Objects which can Handle Dates
                        and Times
colorspace Color Space Manipulation
data.table Extension of Data.frame
dichromat Color Schemes for Dichromats
digest Create Cryptographic Hash Digests of R Objects
doParallel Foreach Parallel Adaptor for the 'parallel'
                        Package
foreach Provides Foreach Looping Construct for R
futile.logger A Logging Utility for R
futile.options Futile options management
ggplot2 An Implementation of the Grammar of Graphics
gplots Various R Programming Tools for Plotting Data
gtable Arrange grobs in tables.
hexbin Hexagonal Binning Routines
impute impute: Imputation for microarray data
IRanges Infrastructure for manipulating intervals on
                        sequences
iterators Provides Iterator Construct for R
labeling Axis Labeling
lambda.r Modeling Data with Functional Programming
limma Linear Models for Microarray Data
lme4 Linear Mixed-Effects Models using 'Eigen' and
                        S4
magrittr A Forward-Pipe Operator for R
MALDIquant Quantitative Analysis of Mass Spectrometry Data
marray Exploratory analysis for two-color spotted
                        microarray data
MSnbase Base Functions and Classes for MS-based
                        Proteomics
MSstats Protein Significance Analysis in DDA, SRM and
                        DIA for Label-free or Label-based Proteomics
                        Experiments
munsell Munsell colour system
mzID An mzIdentML parser for R
mzR parser for netCDF, mzXML, mzData and mzML and
                        mzIdentML files (mass spectrometry data)
pcaMethods A collection of PCA methods
preprocessCore A collection of pre-processing functions
ProtGenerics S4 generic functions for Bioconductor
                        proteomics infrastructure
RColorBrewer ColorBrewer Palettes
Rcpp Seamless R and C++ Integration
reshape Flexibly reshape data.
reshape2 Flexibly Reshape Data: A Reboot of the Reshape
                        Package.
S4Vectors S4 implementation of vectors and lists
scales Scale Functions for Visualization
snow Simple Network of Workstations
stringi Character String Processing Facilities
stringr Simple, Consistent Wrappers for Common String
                        Operations
survival Survival Analysis
vsn Variance stabilization and calibration for
                        microarray data
XML Tools for Parsing and Generating XML Within R
                        and S-Plus
zlibbioc An R packaged zlib-1.2.5

Packages in library ‘C:/Program Files/R/R-3.2.1/library’:

base The R Base Package
bitops Bitwise Operations
boot Bootstrap Functions (Originally by Angelo Canty
                        for S)
caTools Tools: moving window statistics, GIF, Base64,
                        ROC AUC, etc.
class Functions for Classification
cluster Cluster Analysis Extended Rousseeuw et al.
codetools Code Analysis Tools for R
compiler The R Compiler Package
datasets The R Datasets Package
foreign Read Data Stored by Minitab, S, SAS, SPSS,
                        Stata, Systat, Weka, dBase, ...
gdata Various R Programming Tools for Data
                        Manipulation
gplots Various R Programming Tools for Plotting Data
graphics The R Graphics Package
grDevices The R Graphics Devices and Support for Colours
                        and Fonts
grid The Grid Graphics Package
gtools Various R Programming Tools
KernSmooth Functions for Kernel Smoothing Supporting Wand
                        & Jones (1995)
lattice Lattice Graphics
lme4 Linear Mixed-Effects Models using 'Eigen' and
                        S4
MASS Support Functions and Datasets for Venables and
                        Ripley's MASS
Matrix Sparse and Dense Matrix Classes and Methods
methods Formal Methods and Classes
mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML
                        Smoothness Estimation
minqa Derivative-free optimization algorithms by
                        quadratic approximation
nlme Linear and Nonlinear Mixed Effects Models
nloptr R interface to NLopt
nnet Feed-Forward Neural Networks and Multinomial
                        Log-Linear Models
parallel Support for Parallel computation in R
plyr Tools for Splitting, Applying and Combining
                        Data
Rcpp Seamless R and C++ Integration
RcppEigen 'Rcpp' Integration for the 'Eigen' Templated
                        Linear Algebra Library
reshape Flexibly reshape data.
rpart Recursive Partitioning and Regression Trees
spatial Functions for Kriging and Point Pattern
                        Analysis
splines Regression Spline Functions and Classes
stats The R Stats Package
stats4 Statistical Functions using S4 Classes
survival Survival Analysis
tcltk Tcl/Tk Interface
tools Tools for Package Development
translations The R Translations Package
utils The R Utils Package

 Best,
Tobi

Same situation for the Administrator account: MSstats was installed in the private branch of the libPaths:
Packages in library ‘C:/Users/Administrator/Documents/R/win-library/3.2’:

affy Methods for Affymetrix Oligonucleotide Arrays
affyio Tools for parsing Affymetrix data files
Biobase Biobase: Base functions for Bioconductor
BiocGenerics S4 generic functions for Bioconductor
BiocInstaller Install/Update Bioconductor and CRAN Packages
BiocParallel Bioconductor facilities for parallel evaluation
chron Chronological Objects which can Handle Dates
                        and Times
colorspace Color Space Manipulation
data.table Extension of Data.frame
dichromat Color Schemes for Dichromats
digest Create Cryptographic Hash Digests of R Objects
doParallel Foreach Parallel Adaptor for the 'parallel'
                        Package
foreach Provides Foreach Looping Construct for R
futile.logger A Logging Utility for R
futile.options Futile options management
ggplot2 An Implementation of the Grammar of Graphics
gtable Arrange grobs in tables.
hexbin Hexagonal Binning Routines
impute impute: Imputation for microarray data
IRanges Infrastructure for manipulating intervals on
                        sequences
iterators Provides Iterator Construct for R
labeling Axis Labeling
lambda.r Modeling Data with Functional Programming
limma Linear Models for Microarray Data
magrittr A Forward-Pipe Operator for R
MALDIquant Quantitative Analysis of Mass Spectrometry Data
marray Exploratory analysis for two-color spotted
                        microarray data
MSnbase Base Functions and Classes for MS-based
                        Proteomics
MSstats Protein Significance Analysis in DDA, SRM and
                        DIA for Label-free or Label-based Proteomics
                        Experiments
munsell Munsell colour system
mzID An mzIdentML parser for R
mzR parser for netCDF, mzXML, mzData and mzML and
                        mzIdentML files (mass spectrometry data)
pcaMethods A collection of PCA methods
preprocessCore A collection of pre-processing functions
ProtGenerics S4 generic functions for Bioconductor
                        proteomics infrastructure
RColorBrewer ColorBrewer Palettes
reshape2 Flexibly Reshape Data: A Reboot of the Reshape
                        Package.
S4Vectors S4 implementation of vectors and lists
scales Scale Functions for Visualization
snow Simple Network of Workstations
stringi Character String Processing Facilities
stringr Simple, Consistent Wrappers for Common String
                        Operations
vsn Variance stabilization and calibration for
                        microarray data
XML Tools for Parsing and Generating XML Within R
                        and S-Plus
zlibbioc An R packaged zlib-1.2.5

Packages in library ‘C:/Program Files/R/R-3.2.1/library’:

base The R Base Package
bitops Bitwise Operations
boot Bootstrap Functions (Originally by Angelo Canty
                        for S)
caTools Tools: moving window statistics, GIF, Base64,
                        ROC AUC, etc.
class Functions for Classification
cluster Cluster Analysis Extended Rousseeuw et al.
codetools Code Analysis Tools for R
compiler The R Compiler Package
datasets The R Datasets Package
foreign Read Data Stored by Minitab, S, SAS, SPSS,
                        Stata, Systat, Weka, dBase, ...
gdata Various R Programming Tools for Data
                        Manipulation
gplots Various R Programming Tools for Plotting Data
graphics The R Graphics Package
grDevices The R Graphics Devices and Support for Colours
                        and Fonts
grid The Grid Graphics Package
gtools Various R Programming Tools
KernSmooth Functions for Kernel Smoothing Supporting Wand
                        & Jones (1995)
lattice Lattice Graphics
lme4 Linear Mixed-Effects Models using 'Eigen' and
                        S4
MASS Support Functions and Datasets for Venables and
                        Ripley's MASS
Matrix Sparse and Dense Matrix Classes and Methods
methods Formal Methods and Classes
mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML
                        Smoothness Estimation
minqa Derivative-free optimization algorithms by
                        quadratic approximation
nlme Linear and Nonlinear Mixed Effects Models
nloptr R interface to NLopt
nnet Feed-Forward Neural Networks and Multinomial
                        Log-Linear Models
parallel Support for Parallel computation in R
plyr Tools for Splitting, Applying and Combining
                        Data
Rcpp Seamless R and C++ Integration
RcppEigen 'Rcpp' Integration for the 'Eigen' Templated
                        Linear Algebra Library
reshape Flexibly reshape data.
rpart Recursive Partitioning and Regression Trees
spatial Functions for Kriging and Point Pattern
                        Analysis
splines Regression Spline Functions and Classes
stats The R Stats Package
stats4 Statistical Functions using S4 Classes
survival Survival Analysis
tcltk Tcl/Tk Interface
tools Tools for Package Development
translations The R Translations Package
utils The R Utils Package

Thanks, Tobi. I will try to figure out how to fix these problems.

To answer your question, the way that Skyline installs R packages is that it runs an R script which is included with the tool.
Here is that script for MSstats:
https://svn.code.sf.net/p/proteowizard/code/trunk/pwiz/pwiz_tools/Skyline/Executables/Tools/MSstats/tool-inf/InstallPackages.r

I don't know much about how installing packages in R works. Certainly, in the non-admin-install case, we want the R packages to end up in the user's private spot. I imagine Skyline will need to do something clever with R library paths before executing the "InstallPackages.r" script.

Hi Nick,

an update. Although skyline claims that MSstats it is fully installed launching the MSstats/QC workflow results in the following error:

pwiz.Skyline.Model.Tools.ToolExecutionException: Error running the installed tool MSstats\QC. It seems to be missing a file. Please reinstall the tool and try again. ---> System.IO.FileNotFoundException: Could not load file or assembly 'file:///C:\Program Files\Skyline\Tools\MSstats3.2.3.1_external\MSStatArgsCollector.dll' or one of its dependencies. The system cannot find the file specified.
   at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
   at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
   at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
   at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark)
   at System.Reflection.Assembly.LoadFrom(String assemblyFile)
   at pwiz.Skyline.Model.Tools.ToolDescription.CallArgsCollector(Control parent, String args, String reportCsv, String pathReportCsv, ProcessStartInfo startInfo) in c:\Users\nicksh\svn\skyline_3_5_chorusimprovements\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 506
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Model.Tools.ToolDescription.CallArgsCollector(Control parent, String args, String reportCsv, String pathReportCsv, ProcessStartInfo startInfo) in c:\Users\nicksh\svn\skyline_3_5_chorusimprovements\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 581
   at pwiz.Skyline.Model.Tools.ToolDescription.RunExecutableBackground(SrmDocument document, IToolMacroProvider toolMacroProvider, TextWriter textWriter, IProgressMonitor progressMonitor, Control parent) in c:\Users\nicksh\svn\skyline_3_5_chorusimprovements\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 396
   at pwiz.Skyline.Model.Tools.ToolDescription.<>c__DisplayClassa.<RunExecutable>b__9() in c:\Users\nicksh\svn\skyline_3_5_chorusimprovements\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 337

I checked the ...\Skyline\Tools\ folder. No MStstas3.2.3.1. subfolder.

I removed MSstats using Tools -> External tools -> Remove and installed from the tool store again (skyline was run as admin and the path modified as you suggested. There is still an error:

pwiz.Skyline.Model.Tools.ToolExecutionException: Error running the installed tool MSstats\QC. It seems to be missing a file. Please reinstall the tool and try again. ---> System.IO.FileNotFoundException: Could not load file or assembly 'file:///C:\Program Files\Skyline\Tools\MSstats3.2.3.1_external\MSStatArgsCollector.dll' or one of its dependencies. The system cannot find the file specified.
   at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
   at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
   at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
   at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark)
   at System.Reflection.Assembly.LoadFrom(String assemblyFile)
   at pwiz.Skyline.Model.Tools.ToolDescription.CallArgsCollector(Control parent, String args, String reportCsv, String pathReportCsv, ProcessStartInfo startInfo) in c:\Users\nicksh\svn\skyline_3_5_chorusimprovements\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 506
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Model.Tools.ToolDescription.CallArgsCollector(Control parent, String args, String reportCsv, String pathReportCsv, ProcessStartInfo startInfo) in c:\Users\nicksh\svn\skyline_3_5_chorusimprovements\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 581
   at pwiz.Skyline.Model.Tools.ToolDescription.RunExecutableBackground(SrmDocument document, IToolMacroProvider toolMacroProvider, TextWriter textWriter, IProgressMonitor progressMonitor, Control parent) in c:\Users\nicksh\svn\skyline_3_5_chorusimprovements\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 396
   at pwiz.Skyline.Model.Tools.ToolDescription.<>c__DisplayClassa.<RunExecutable>b__9() in c:\Users\nicksh\svn\skyline_3_5_chorusimprovements\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 337

I checked for the ...\Tools directory again. Looks ok now:

01/11/16 03:27 PM <DIR> .
01/11/16 03:27 PM <DIR> ..
10/27/15 04:33 PM 37,888 MSStatArgsCollector.dll
10/27/15 04:33 PM 56,832 MSStatArgsCollector.pdb
11/18/15 08:30 AM 8,303 MSStatsDSS.r
11/18/15 08:29 AM 6,418 MSStatsGC.r
11/18/15 08:29 AM 4,434 MSStatsQC.r
11/05/15 06:23 PM <DIR> tool-inf
               5 File(s) 113,875 bytes
               3 Dir(s) 7,311,114,240 bytes free

C:\Program Files\Skyline\Tools\MSstats3.2.3.1_external>

So the dll is there and all the R scripts...what else can I do to get MSstsats running?

Got it to work. I think your path modification was not correct. I used:

path %path%;"C:\Program Files\Skyline"

now skyline is starting up by calling "skyline" on the cmd

maybe it needs a capital C for the volume?

I think it is going to be a lot of work to make it so that an administrator is able to install external tools in Skyline, and then have those tools be available to other users on the machine.

When Skyline installs an external tool, it copies some files into
C:\Program Files\Skyline\Tools

It also saves some settings in the user's profile directory that indicate that the tool was installed, and also things like which version of R and which packages are installed.
When another user comes along, there are the files in "C:\Program Files\Skyline\Tools", but they don't have any of the other settings to make the external tool actually work.

At first I thought it would be straightforward to just change some of these "per user" settings and turn them into "per application" settings.
However, when you install an external tool, it potentially changes a bunch of other settings such as the list of report definitions, or the set of annotations.

We have two choices for how this should work:
1. External tools no longer get installed in "C:\Program Files\Skyline\Tools". Instead, they get installed somewhere in the user's home directory (somewhere under "C:\Users\username\AppData"). Each user on your computer is responsible for installing the external tools that they need.
2. When administrators install external tools, they have the option of either installing them in "C:\Program Files\Skyline\Tools" where they will be shared by all users, or in their own home directory. There are other settings such as the report definitions (File > Export > Report) or annotations (Settings > Document Settings) where administrators are able to choose whether their change affects all users.

#1 is a straightforward thing to implement at this point, but I'm worried it might defeat the purpose of having the Administrator Install-- if users have to install their own external tools, what have you really saved by having a per-machine install of Skyline?

#2 is quite a bit of work.

What do you think?

Hi Tobi and Nick,

I follow your discussion with attention.
If I may give my point of you: the purpose of installing Skyline and its external tools on a server was to process the installation once and be aware of the versions installed (and having a homogeneous environment for any user).
So, first thanks for having provided the installer.

Considering:
- our goal: the best would be the choice #2 with an installation in "C:\Program Files\Skyline\Tools" and not in any user's home directory.
- the development work: the choice #1 would be sufficient if we process as following (please correct if necessary):
(1) a single installation for Skyline done by the administrator in "C:\Program Files\Skyline" (with Skyline available for any users)
(2) an installation of external tools, also done by the administrator in its user's home directory. The administrator should then copy the "Tools" directory in any other user's session (we have less than 5 users so this solution still limits administration interventions and we only use MSStats and QUASAR occasionally).

Best regards,
Oana

Hello,

in the meantime I am the sysadmin of Tobias and responsible for installing Skyline on a bunch of computers, where users should be able to use skyline.

It seems that the problems noted above are still not solved in version 4.1 of skyline.

As we have about 4000 users, we have to use "roaming profiles" on our windows computers.
With roaming profiles, the folder "c:\users\username" is removed on logout!
And together with this the complete skyline installation of the user is gone, including the config file.

With an admin install, at least the skyline itself can be installed on the host.

But now the "Tools" come in to the game.

It might be possible to give the user full control on the "c:\program files\skyline\tools" directory, which makes it possible to install the Tools (sometimes) in this directory. Unfortunately the config is still in the local part of the users profile. After logout the files are still in the "tools" directory, but Skyline does not show them anymore, because the config was removed.

In the current situation, the user has to install his Tools again and again and again on every login, including the fine tuned configuration.

As this discussion is now 2 years old and still the software is not "roaming profile" friendly, i think it is best I script something, that the user can install the things with one click.