Deprecated library ?

[CarlJF]

Hi,

I'm trying to run SPADE from the CytoScape plugin using the data from the Nat Biotech article. When clicking on "Run Spade", the execution console appears and I get an error message telling:

In SPADE.driver(FILE_TO_PROCESS, file_pattern = "*.fcs", out_dir = OUTPUT_DIR, :
arcsinh_cofactor is deprecated, use transform=flowCore::arcsinhTransform(...) instead

I'm using CytoScape 2.8.3 and R 2.15.1.

Is there something that can be done about this ?

[zbjornson]

Hello,
Looks like the plugin and the R back end are out of sync in the latest release. You can manually change the runSPADE.r file to use the syntax shown in that message using a text editor if you want to run this very soon. I'll make the fix to the plugin tomorrow and let you know on here as soon as I do.
Sorry about that,
Zach

[CarlJF]

OK thanks!

I will wait the fix and rebuild the plugin.

[zbjornson]

Hello,

It turns out that SPADE will run fine despite this warning. If you ignore the message, the analysis should complete. I'll make future plugins not generate this warning, but don't worry about updating your plugin meanwhile.

Thanks,
Zach

[CarlJF]

Then, there's probably something wrong either with my installation or with the way I try to run Spade. I get a window with the message "Execution failed. See output dialog for clues.". I supposed that the Output dialog was the Spade execution console, with the first error message in this thread. Or is this "dialog output" something else ? A log file ?

[zbjornson]

That's the correct dialog to be looking at. Are there any other messages? (Perhaps copy-and-paste the whole contents of the dialog.)

[CarlJF]

Here's a copy of the console. Note that I have R in french, thus some part are in french and I added the translation between ():

Le chargement a nécessité le package : igraph0 (Loading needed package: igraph0)
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)

Message d'avis :
Pas de fonction correspondant aux méthodes exportées de 'rrcov' pour : 'show' (No function corresponding to methods exported from 'rrcov/' for 'show/')
Downsampling file: ./nbt.1991-SD1.fcs
Message d'avis :
In SPADE.driver(FILE_TO_PROCESS, file_pattern = "*.fcs", out_dir = OUTPUT_DIR, :
arcsinh_cofactor is deprecated, use transform=flowCore::arcsinhTransform(...) instead
Exécution arrêtée (Execution halted)

And here's a copy of the Summary and Run window:

Directory: C:\Users\Carl\Documents\FCS Data
Clustering Parameters:
Arcsinh Cofactor: 150
Downsample Percentile: 5
Target Number of Clusters: 50
Clustering Markers: marker1::marker1, marker2::marker2
Panels:
catchall:
Panel Files: C:\Users\Carl\Documents\FCS Data\nbt.1991-SD1.fcs
Median Markers: All
Reference Files:
Fold-change Markers:

Hope these helps!
Thanks!

[zbjornson]

Thanks for sending the log. I missed in your original post that you're using R 2.15. Unfortunately SPADE needs R 2.14 because some of the libraries that SPADE depends on are not yet available for R 2.15.

R 2.14 is available here: http://stat.ethz.ch/CRAN/bin/windows/base/old/2.14.2/
Please install that version, then re-install SPADE.

Sorry about that.
-Zach

[CarlJF]

Ok, I will change my version of R.

However if Spade is not actually working with 2.15, it may be a good idea to update your wiki page (https://github.com/nolanlab/spade/wiki/GettingStarted) with this information. Actually, this page rather says to use 2.15 or later...

[zbjornson]

Hrm, I'm checking with the other developers if you want to wait to downgrade R.

I just tried installing SPADE in R 2.15 and that failed, whereas I was able to run it in R 2.14 though.

Stand by... sorry for the confusion.

[zbjornson]

Hello again -- When you installed SPADE, did you use a download from github or did you use this method: install.packages("spade", repos=c("http://cran.fhcrc.org/","http://bioconductor.org/packages/2.11/bioc"))
?

We're trying to figure out the source of the error you posted still... sorry for the delay.

Thanks,
Zach

[CarlJF]

I use the install.package... method. I just copied/pasted the command from the Getting Started webpage to the R console.

[CarlJF]

Some more precisions to help you, the installed R version is 2.15.1 for Windows 64-bits. The OS is Windows 7 64-bits.

[zbjornson]

Thank you. We've finally identified the issue, I've made a fix, and we're testing it. Should have a fix to you very soon. Meanwhile, we've realized that you can still run the runSPADE.R file generated by the Cytoscape plugin from the command line:

R -f runSPADE.R

[zbjornson]

Hello,

A corrected plugin is available here:
https://github.com/nolanlab/spade/blob/1f9d5a5cfeb94a1e7656992cdf5e22c51ac06883/inst/tools/CytoSPADE.jar

Please download this and put it in the Cytoscape plugins directory located approximately here:
C:\Program Files\Cytoscape_v2.8.3\plugins

Thanks, and sorry for the troubles.
Zach

[CarlJF]

Hello,

I've updated the plugin and it works up to a point when I get following error message:

#BEGIN AUTOGENERATED DATA
FILE_TO_PROCESS="."
CLUSTERING_MARKERS=c("marker1","marker2")
PANELS=list(

• list(
• panel_files=c("nbt.1991-SD1.fcs"),
• median_cols=NULL,
• reference_files=NULL,
• fold_cols=NULL
• ))
  TRANSFORMS=flowCore::arcsinhTransform(a=0, b=0,006667)
  Scalable Robust Estimators with High Breakdown Point (version 1.3-02)

Erreur dans checkSlotAssignment(object, name, value) :
assignment of an object of class "numeric" is not valid for slot "transformationId" in an object of class "transform"; is(value, "character") is not TRUE
Calls: -> @<- -> slot<- -> checkSlotAssignment

And then, execution stops... Any idea ?

[zbjornson]

Hello,

That appears to be a localization issue with R. The statement flowCore::arcsinhTransform(a=0, b=0,006667) throws that error; b=0.006667 (with a period instead of a comma) is expected.

Perhaps try running R in English mode, or edit your runSPADE.R file to use periods. I'll look into making the plugin safe for use in locales that use commas as decimal separators.

Best,
Zach

[zbjornson]

Correction -- running R in English-mode won't fix this. The plugin and Cytoscape (e.g. Java) needs to be run in English-mode. I haven't changed this before, but this looks like it might provide guidance:
http://java.com/en/download/help/locale.xml

[CarlJF]

OK, I've try to change , for . in the locale settings but still get the error message...

So, I tried to install Cytospade on Ubuntu with US settings. However, I rapidly got a problem since Spade doesn't want to install in R. After entering:

install.packages("spade", repos=c("http://cran.fhcrc.org/","http://bioconductor.org/packages/2.11/bioc"))

I get the following error messages when R try to install a package named "rgl":

• installing source package ‘rgl’ ...
  ** package ‘rgl’ successfully unpacked and MD5 sums checked
  checking for gcc... gcc -std=gnu99
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables...
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether gcc -std=gnu99 accepts -g... yes
  checking for gcc -std=gnu99 option to accept ISO C89... none needed
  checking how to run the C preprocessor... gcc -std=gnu99 -E
  checking for gcc... (cached) gcc -std=gnu99
  checking whether we are using the GNU C compiler... (cached) yes
  checking whether gcc -std=gnu99 accepts -g... (cached) yes
  checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed
  checking for libpng-config... yes
  configure: using libpng-config
  configure: using libpng dynamic linkage
  checking for X... no
  configure: error: X11 not found but required, configure aborted.
  ERROR: configuration failed for package ‘rgl’
• removing ‘/home/carl/R/i686-pc-linux-gnu-library/2.15/rgl’
  ERROR: dependency ‘rgl’ is not available for package ‘ks’
• removing ‘/home/carl/R/i686-pc-linux-gnu-library/2.15/ks’
  ERROR: dependency ‘ks’ is not available for package ‘feature’
• removing ‘/home/carl/R/i686-pc-linux-gnu-library/2.15/feature’
  ERROR: dependency ‘feature’ is not available for package ‘flowCore’
• removing ‘/home/carl/R/i686-pc-linux-gnu-library/2.15/flowCore’
  ERROR: dependency ‘flowCore’ is not available for package ‘spade’
• removing ‘/home/carl/R/i686-pc-linux-gnu-library/2.15/spade’

The downloaded source packages are in
‘/tmp/RtmpPhHKVF/downloaded_packages’
Warning messages:
1: In install.packages("spade", repos = c("http://cran.fhcrc.org/", :
installation of package ‘rgl’ had non-zero exit status
2: In install.packages("spade", repos = c("http://cran.fhcrc.org/", :
installation of package ‘ks’ had non-zero exit status
3: In install.packages("spade", repos = c("http://cran.fhcrc.org/", :
installation of package ‘feature’ had non-zero exit status
4: In install.packages("spade", repos = c("http://cran.fhcrc.org/", :
installation of package ‘flowCore’ had non-zero exit status
5: In install.packages("spade", repos = c("http://cran.fhcrc.org/", :
installation of package ‘spade’ had non-zero exit status

I'm not sure if the problem came from R or Spade, but it seems that, for whatever reason, it thinks that X11 is not there. Which obviously isn't the case since the OS is working with the graphical interface...

Have you seen this before ? Or do you have a linux distribution to recommend on which you know Cytospade works ?

Thanks!

[zbjornson]

First: I'm surprised changing locale didn't work. If you run the following command in the directory with your runSPADE.R file, it should change the commas to periods (which you could do by-hand as well):

sed 's/\([0-9]\),\([0-9]\)/\1\.\2/g' runSPADE.R > runSPADE.R

and then you can execute it using /.runSPADE.R.

Re: X11. I haven't seen this, and we run SPADE on several linux distributions. It looks like the command sudo apt-get build-dep r-cran-rgl will resolve the issue. (That's a shell command, not an R command.)

Thanks for your perseverance! Hope this works.
Zach

[CarlJF]

Thanks!

Cytospade is now working after installing the rgl package.

[zbjornson]

Hello CarlJF,

The issue with commas and periods has been fixed in the latest version of the SPADE plugin. If you wish, you can reinstall SPADE using the instructions in the wiki or do this:

1. Download this file: https://github.com/nolanlab/spade/raw/master/inst/tools/CytoSPADE.jar
2. Put that file in your Cytoscape plugins directory. This is probably C:\Program Files\Cytoscape_v2.8.3\plugins for you. Click "ok" or "replace" to acknowledge that you're replacing the existing file with the same name.

Thanks,
Zach