Hi all, As promised, I released a first quite advanced (burn proof enough, just hopping for now) for an 'Rserve wrapper'. Keeping it handy and with good performances under Windows gave me quite a hard time, but I hope this first attempt is a minimum satisfying. You'll tell me...
Rserve impl. change log: ----------------------- [Still limited to the 'BaselineCorrectionModule' area - Backward compatibility with 'JRI' preserved] * 'R_HOME' detection: If not found automatically, R_HOME must be set (from startMZmine script). * Dedicated exception handling (R, Rserve or required package not found, mostly via the 'RSessionWrapperException'). * Fixed some windows specifics (multi-instance open(), close(), cancel(), bruteCancel()...). * Cleaned console logging and GUI errors feedback. * Cleanup everything related to 'Rserve' on MZmine exit. * Cleaned up source code and comments. * Removed completely RCaller stuffs. * Still can choose preferred R engine among JRIengine and Rserve. Release download location: ------------------------- https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141209.zip Thanks by advance for your feedback. Cheers Gauthier Note: Since I haven't been updating from trunk since the middle of the 2.11, there might be some incompatibilities with 2.12. Having this branch up to date is my next priority. I'll also be glad to help with working on the trunk to get 'Rserve' integrated, in case you find what I did with the branch convincing. [Tomas]: Have you been looking deeper into 'Renjin'? Is it still an option, something we should dig into? On 12/04/2014 07:59 AM, Tomas Pluskal wrote: > Hi Gauthier, > > I tried running your build _without_ installing the Rserve package first. I > got some exceptions in the console: > > [15:44:20|INFO|RSessionWrapper]: Please install Rserve manually in your R > environment using "install.packages('Rserve',,'http://www.rforge.net/')" > command. > Please install Rserve manually in your R environment using > "install.packages('Rserve',,'http://www.rforge.net/')" command. > Connecting R://localhost ... no: Cannot connect: Connection refused > Connection R://localhost failed. > [15:44:21|INFO|RSessionWrapper]: Failed to launch local Rserve. Unable to > initialize Rsession. > Failed to launch local Rserve. Unable to initialize Rsession. > java.lang.IllegalArgumentException: Failed to launch local Rserve. Unable to > initialize Rsession. > at org.math.R.Rsession.begin(Rsession.java:408) > at org.math.R.Rsession.startup(Rsession.java:337) > at org.math.R.Rsession.<init>(Rsession.java:329) > at org.math.R.Rsession.newInstanceTry(Rsession.java:300) > at > net.sf.mzmine.util.RSessionWrapper.getRengineInstance(RSessionWrapper.java:145) > at net.sf.mzmine.util.RSessionWrapper.open(RSessionWrapper.java:317) > at > net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionTask.run(BaselineCorrectionTask.java:126) > at net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60) > [15:44:21|SEVERE|BaselineCorrectionTask]: Unknown baseline correction > error.(java.lang.IllegalStateException: This feature requires R but it > couldn't be loaded (Failed to launch local Rserve. Unable to initialize > Rsession.)@net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionTask.run(BaselineCorrectionTask.java:129)) > [15:44:21|SEVERE|WorkerThread]: Unhandled exception > java.lang.NullPointerException while processing task Correcting baseline for > A(java.lang.nullpointerexcept...@net.sf.mzmine.util.RSessionWrapper.close(RSessionWrapper.java:409)) > java.lang.NullPointerException > at net.sf.mzmine.util.RSessionWrapper.close(RSessionWrapper.java:409) > at > net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionTask.run(BaselineCorrectionTask.java:176) > at net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60) > > > IMHO it is better to avoid using the IllegalArgumentException or other > undeclared runtime exceptions. If your code might fail, then please declare > properly the exceptions it might throw. > > After installing the Rserve package, everything is running smoothly. > Although, it still requires the R_HOME variable to be set. If I don't set it, > I get this error: > > [15:52:14|INFO|RSessionWrapper]: Rserve R://localhost is not accessible. > [15:52:14|INFO|RSessionWrapper]: Trying to spawn R://localhost > [15:52:14|INFO|RSessionWrapper]: Environment variables: > R_HOME=/usr/lib/R/ > java.lang.IllegalArgumentException: R_HOME environment variable not correctly > set. > You can set it using 'java ... -DR_HOME=[Path to R] ...' startup command. > at org.math.R.Rdaemon.start(Rdaemon.java:218) > at org.math.R.Rsession.begin(Rsession.java:392) > at org.math.R.Rsession.startup(Rsession.java:337) > at org.math.R.Rsession.<init>(Rsession.java:329) > at org.math.R.Rsession.newInstanceTry(Rsession.java:300) > at > net.sf.mzmine.util.RSessionWrapper.getRengineInstance(RSessionWrapper.java:145) > at net.sf.mzmine.util.RSessionWrapper.open(RSessionWrapper.java:317) > at > net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.BaselineCorrectionTask.run(BaselineCorrectionTask.java:126) > at net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60) > > > Anyway, I think this Rserve solution looks much better than the JRI interface > that is currently used. > > Best regards, > > Tomas > > > > On Dec 4, 2014, at 4:32, Gauthier Boaglio <gauthier.boag...@gmail.com> wrote: > >> Hi, >> >> For the record, "Rsession" did the trick. With some little drawbacks - >> fixable small ones - for UNIX platforms. I'll see that later. Here's a >> release working theoretically on all platforms with Java 1.7 or higher: >> >> https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141203.zip >> >> Cheers >> Gauthier >> >> >> On 12/03/2014 05:17 AM, Tomas Pluskal wrote: >>> Hi Gauthier, >>> >>> I think another option to consider seriously is Renjin. Although Renjin in >>> its current development state does not really support installation of >>> packages, we could simply copy & paste the relevant functions from the >>> existing R packages. >>> If that works, no configuration or platform-specific hacks would be >>> necessary, as Renjin is pure java. >>> >>> Cheers, >>> >>> Tomas >>> >>> >>> >>> >>> >>> >>> On Dec 3, 2014, at 12:44, Gauthier Boaglio <gauthier.boag...@gmail.com> >>> wrote: >>> >>>> I just went through "rSession" code again and a bit further, and I might >>>> have spoken too fast. >>>> Mainly classes "Rsession" and "RserverConf" seems to speak about things >>>> like "windows multi-session emulation", playing with ports, etc. (Sounds >>>> like exactly what I was trying to describe previously, isn't it?). >>>> I'll have a new fresh eye on it tomorrow (that could avoid to reinvent the >>>> wheel). 5AM over here... >>>> >>>> Cheers >>>> Gauthier >>>> >>>> >>>> -------- Forwarded Message -------- >>>> Subject: Re: [Mzmine-devel] R usage in MZmine - What about replacing >>>> JRIengine? - Not working well under Windows. >>>> Date: Wed, 03 Dec 2014 04:29:34 +0100 >>>> From: Gauthier Boaglio <gauthier.boag...@gmail.com> >>>> To: mzmine-devel@lists.sourceforge.net >>>> >>>> Hi Tomas, >>>> >>>> Yes I have, and it really doesn't help that much, that is why I preferred >>>> implementing my own minimalistic class. I might change my mind at some >>>> point, but I don't believe adding this dependency corresponds to an actual >>>> need. >>>> >>>> Otherwise, I have some news about Rserve (quite bad ones). It relies on >>>> unix features and is not able, under windows, to 'fork' instances like >>>> unix systems do. This is quite deceiving. But, I am implementing a >>>> workaround: windows specific solution to mimic processes forking. We'll >>>> see if it is convincing once I have it working. >>>> Since we still can run several instances of Rserve main server under >>>> windows (despite we cannot use the great UNIX features), the idea is: >>>> >>>> Creating a pool of a finite number of warm instances of Rserve - 8 is a >>>> good number I suppose, ready for use (and started at the application >>>> startup, or at the very first time R is required). Those instances would >>>> have to be mapped on dedicated/respective ports (one for each worker of >>>> the pool). Those port should be chosen among "IANA Registered but marked >>>> as UNASSIGNED ports, if I'm correct. As long as we don't need more workers >>>> than the default warm ones, we manage the pool, >>>> reserving and releasing them on demand. If the amount of concurrent R >>>> tasks required increases, we still can scale the size (number of >>>> active/alive workers) of the pool. When no more R task is running, we can >>>> then scale back to normal, and put the default number of warm workers to >>>> sleep. >>>> >>>> I am a bit tired, so my apologies if my English is getting odd, but I hope >>>> that what I am telling here is clear enough. >>>> So, to make it short: Rserve is not ideal (well, it is, but windows >>>> isn't). At least, I found nothing better anywhere. A workaround can be >>>> concidered, which I am going to implement for my own needs anyway, so >>>> you'll have the occasion to test it quite soon. >>>> >>>> I'll check again if "Rsession" doesn't provides the features I am working >>>> on already, but I'm pretty sure it doesn't. >>>> >>>> So, what do you say? To my opinion, with a good handy wrapper, all this >>>> could be viable... >>>> If you have any idea or suggestion about all this. Please tell me such >>>> that I can integrate into my reflections. >>>> >>>> Cheers >>>> Gauthier >>>> >>>> >>>> >>>> >>>> On 12/03/2014 01:54 AM, Tomas Pluskal wrote: >>>>> Hi Gauthier, >>>>> >>>>> Just wondering - have you checked the Rsession project? >>>>> (https://code.google.com/p/rsession/) >>>>> I don't have any personal experience with it, but it seems to contain the >>>>> code to run the Rserve from java. >>>>> >>>>> Cheers, >>>>> >>>>> Tomas >>>>> >>>>> >>>>> On Dec 3, 2014, at 3:43, Gauthier Boaglio <gauthier.boag...@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> My apologies to those who tried to test (hope none of you actually) the >>>>>> release linked above under Windows. This is working under Linux, but not >>>>>> (completely) under Windows. >>>>>> Sorry about that. I try to fix it ASAP and keep you informed. >>>>>> >>>>>> Cheers >>>>>> Gauthier >>>>>> >>>>>> >>>>>> >>>>>> On 12/02/2014 11:47 AM, Gauthier Boaglio wrote: >>>>>>> Text formatted message (for non HTML mailers) >>>>>>> >>>>>>> >>>>>>> -------- Forwarded Message -------- >>>>>>> Subject: R usage in MZmine - What about replacing JRIengine to get >>>>>>> multi-threading support? >>>>>>> Date: Tue, 02 Dec 2014 11:36:55 +0100 >>>>>>> From: Gauthier Boaglio <gauthier.boag...@gmail.com> >>>>>>> To: mzmine-devel@lists.sourceforge.net >>>>>>> >>>>>>> >>>>>>> Hi everyone, >>>>>>> >>>>>>> I begun to use Rserve (multi-threaded), instead of JRIengine (singleton >>>>>>> / mono-threaded), in my personal experimental branch and really think >>>>>>> we could replace JRIengine (which does not take advantage of parallel >>>>>>> tasks processing, as you know), by the former. >>>>>>> I released a version using Rserve (restricted to the "Baseline >>>>>>> Correction Module"). If you want to give it a try, here it is: >>>>>>> https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141128.zip >>>>>>> >>>>>>> Main points: >>>>>>> ----------- >>>>>>> >>>>>>> * Requirements: >>>>>>> ------------ >>>>>>> >>>>>>> No changes in "startMZmine" script (we just need to locate >>>>>>> "R_HOME", as usual). >>>>>>> The only requirement is to have the "Rserve" R package installed. >>>>>>> Then it is ran through a simple R command, looking like: >>>>>>> library(Rserve);Rserve(debug=TRUE/FALSE, >>>>>>> args="--RS-enable-control") >>>>>>> # Where '--RS-enable-control' is used and mandatory to enable >>>>>>> sending "SIGKILL/SIGTERM" to the Rserve instances >>>>>>> # (when we need to abort a blocking 'eval' being performed) >>>>>>> (Note: we already had to install "rJava" for using JRI). So this >>>>>>> does not stand for a big additional constraint for the user. >>>>>>> >>>>>>> => The Rserve runnable (server app.) comes with the said R package >>>>>>> >>>>>>> Note: I believe we could even simplify the "startMZmine" workflow, >>>>>>> by first trying to detect the R location automatically. >>>>>>> (the environment variables to be assigned in the script would >>>>>>> be used only as a fallback in case the detection failed) >>>>>>> >>>>>>> That would more or less look like (See: RUtilities.java) : >>>>>>> >>>>>>> public static String getRexecutablePath() { >>>>>>> >>>>>>> String osname = System.getProperty("os.name"); >>>>>>> if (osname != null && osname.length() >= 7 && >>>>>>> osname.substring(0,7).equals("Windows")) { >>>>>>> LOG.log(Level.INFO, "Windows: query registry to >>>>>>> find where R is installed ..."); >>>>>>> String installPath = null; >>>>>>> try { >>>>>>> Process rp = Runtime.getRuntime().exec("reg >>>>>>> query HKLM\\Software\\R-core\\R"); >>>>>>> StreamHog regHog = new >>>>>>> StreamHog(rp.getInputStream(), true); >>>>>>> rp.waitFor(); >>>>>>> regHog.join(); >>>>>>> installPath = regHog.getInstallPath(); >>>>>>> } catch (Exception rge) { >>>>>>> LOG.log(Level.SEVERE, "ERROR: unable to run >>>>>>> REG to find the location of R: "+rge); >>>>>>> return null; >>>>>>> } >>>>>>> if (installPath == null) { >>>>>>> LOG.log(Level.SEVERE, "ERROR: canot find path >>>>>>> to R. Make sure reg is available and R was installed with registry >>>>>>> settings."); >>>>>>> return null; >>>>>>> } >>>>>>> return installPath + "\\bin\\R.exe"; >>>>>>> } >>>>>>> >>>>>>> File f = new >>>>>>> File("/Library/Frameworks/R.framework/Resources/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/usr/local/lib/R/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/usr/lib/R/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/sw/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/usr/common/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/opt/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> >>>>>>> >>>>>>> return null; >>>>>>> >>>>>>> } >>>>>>> >>>>>>> >>>>>>> * The way it works: >>>>>>> ---------------- >>>>>>> >>>>>>> Rserve is a server (implements a communication protocol with R) >>>>>>> and, to keep it simple, it should be run on localhost and default >>>>>>> port 6311 (this is something that should probably be mentioned to >>>>>>> the user, for security and eventually firewall configuration reasons). >>>>>>> Each time we create a new "RConnection", the main instance of >>>>>>> Rserve starts a new child process. >>>>>>> - We can store the PID of this instance for later termination. >>>>>>> - We can run asynchronously as many instances as we want (as long >>>>>>> as we take care to close/terminate the ones that are no longer used). >>>>>>> >>>>>>> => I already implemented a basic wrapper (that should be enhanced) >>>>>>> for those operations: >>>>>>> >>>>>>> https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/src/main/java/net/sf/mzmine/util/RSession.java >>>>>>> (Simplified version of the class in attachment). >>>>>>> >>>>>>> => The code for starting Rserve main server instance is located in >>>>>>> "RUtilities.java" for now: >>>>>>> >>>>>>> https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/src/main/java/net/sf/mzmine/util/RUtilities.java >>>>>>> >>>>>>> => USAGE (a sample use case can be found in the >>>>>>> BaselineCorrectionTask.java): >>>>>>> >>>>>>> Basically, evaluating one or more R commands is done as >>>>>>> follows: >>>>>>> >>>>>>> - Create and open a new session: >>>>>>> // (This will automatically start Rserve, if not >>>>>>> already running, and open a new slave instance for this task) >>>>>>> String[] reqPackages = new String[] { "ptw" }; >>>>>>> RSession rSession = new RSession(reqPackages); >>>>>>> rSession.open(); >>>>>>> >>>>>>> - Check the additional packages necessary to perform the >>>>>>> commands for the given session: >>>>>>> // Returns the first failing required package name or >>>>>>> null if successful >>>>>>> String missingPackage = >>>>>>> rSession.loadRequiredPackages(); >>>>>>> >>>>>>> - Do some R evaluations, such as: >>>>>>> // Set chromatogram. >>>>>>> rSession.assignDoubleArray("chromatogram", >>>>>>> chromatogram); >>>>>>> // Calculate baseline. >>>>>>> rSession.eval("baseline <- asysm(chromatogram," + >>>>>>> smoothing + "," + asymmetry + ")"); >>>>>>> baseline = rSession.collectDoubleArray("baseline"); >>>>>>> >>>>>>> - Release the session (closes the socket connection for >>>>>>> the session and ends the related Rserve slave process): >>>>>>> rSession.close(false); >>>>>>> >>>>>>> Note: We should also check, at some point, if no more >>>>>>> tasks are requiring Rserve, and shutdown the server. >>>>>>> (it will be restarted the next time we use a >>>>>>> MZmine feature requiring R anyway...) >>>>>>> >>>>>>> * Performance considerations: >>>>>>> -------------------------- >>>>>>> >>>>>>> Source: >>>>>>> http://www.sciencedomain.org/download.php?f=Satman4152014BJMCS10902_1.pdf&aid=4838&type=a >>>>>>> >>>>>>> The performances where good enough for what I had to do with the >>>>>>> BaselineCorretors. So, at very first sight, this should fit the other >>>>>>> needs >>>>>>> (anyway, the other very few multi-threaded alternatives I gave a test >>>>>>> where not exploitable in term of evaluation speed). >>>>>>> May be we should/will have to consider switching between JRIengine and >>>>>>> Rserve for some particular features). I hope not, but in any case, >>>>>>> this is something which seems doable: as far as I tested, there is >>>>>>> absolutely no incompatibilities between Rserve and JRI. >>>>>>> >>>>>>> To make your own opinion on all this, the BaselineCorretorModule >>>>>>> (again) allows to choose the R engine among RCaller (Online), JRIengine >>>>>>> and Rserve. >>>>>>> Just run the MZmine version linked on top of this email, and go to "Raw >>>>>>> data methods > Filtering > Baseline Correction" >>>>>>> >>>>>>> >>>>>>> >>>>>>> Fill free to ask if something is unclear or if you have any further >>>>>>> questionings. >>>>>>> Looking forward to your constructive comments and thoughts... >>>>>>> >>>>>>> I'll be glad to help, as much as possible, with migrating to Rserve (if >>>>>>> it turns out that this solution really is viable). >>>>>>> >>>>>>> Cheers >>>>>>> Gauthier >>>>>>> >>>>>>> >>>>>>> >>>>>>> -------- Forwarded Message -------- >>>>>>> Subject: Re: [Mzmine-devel] Baseline correction >>>>>>> Date: Tue, 2 Dec 2014 05:15:41 +0000 >>>>>>> From: Tomas Pluskal <plus...@oist.jp> >>>>>>> To: Gauthier Boaglio <gauthier.boag...@gmail.com> >>>>>>> >>>>>>> >>>>>>> Hi Gauthier, >>>>>>> Now that we released version 2.12, I think it is a good time to >>>>>>> consider making the switch from JRI to RServe. >>>>>>> I think it is a good idea - I don't really like the current JRI >>>>>>> interface. >>>>>>> It would be great if you could send a message to the devel list, where >>>>>>> you can summarize what you found about RServe. Especially, we would >>>>>>> like to know >>>>>>> 1) is the initial setup and configuration going to be easier than the >>>>>>> current one (is it necessary to edit the startMZmine script in order to >>>>>>> use RServe?) >>>>>>> 2) how does the actual code differ between RServe and JRI? >>>>>>> Thanks a lot! >>>>>>> Cheers, >>>>>>> Tomas >>>>>>> =============================================== >>>>>>> Tomas Pluskal >>>>>>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate >>>>>>> University >>>>>>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan >>>>>>> WWW: https://groups.oist.jp/g0 >>>>>>> TEL: +81-98-966-8684 >>>>>>> Fax: +81-98-966-2890 >>>>>>> >>>>>>> -- >>>>>>> Gauthier BOAGLIO >>>>>>> CEFE - UMR 5175 >>>>>>> 1919 route de Mende >>>>>>> F-34293 Montpellier cedex 5 >>>>>>> >>>>>>> Tel: +33/0 4 67 61 32 15 >>>>>>> Fax: +33/0 4 67 61 33 36 >>>>>>> >>>>>>> email: gauthier.boag...@cefe.cnrs.fr >>>>>>> www: >>>>>>> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio >>>>>>> http://www.evolepid.org/people.php?name=boaglio >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -------- Forwarded Message -------- >>>>>>> Subject: R usage in MZmine - What about replacing JRIengine to >>>>>>> get multi-threading support? >>>>>>> Date: Tue, 02 Dec 2014 11:36:55 +0100 >>>>>>> From: Gauthier Boaglio <gauthier.boag...@gmail.com> >>>>>>> To: mzmine-devel@lists.sourceforge.net >>>>>>> >>>>>>> Hi everyone, >>>>>>> >>>>>>> I begun to use Rserve (multi-threaded), instead of JRIengine (singleton >>>>>>> / mono-threaded), in my personal experimental branch and really think >>>>>>> we could replace JRIengine (which does not take advantage of parallel >>>>>>> tasks processing, as you know), by the former. >>>>>>> I released a version using Rserve (restricted to the "Baseline >>>>>>> Correction Module"). If you want to give it a try, here it is: >>>>>>> >>>>>>> https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141128.zip >>>>>>> >>>>>>> Main points: >>>>>>> ----------- >>>>>>> >>>>>>> * Requirements: >>>>>>> >>>>>>> ------------ >>>>>>> >>>>>>> >>>>>>> No changes in "startMZmine" script >>>>>>> (we just need to locate "R_HOME", as usual). >>>>>>> The only requirement is to have the "Rserve" R package >>>>>>> installed. Then it is ran through a simple R command, looking like: >>>>>>> library(Rserve);Rserve(debug=TRUE/FALSE, >>>>>>> args="--RS-enable-control") >>>>>>> # Where '--RS-enable-control' is used and mandatory to >>>>>>> enable sending "SIGKILL/SIGTERM" to the Rserve instances >>>>>>> # (when we need to abort a blocking 'eval' being >>>>>>> performed) >>>>>>> (Note: we already had to install "rJava" for using JRI). So >>>>>>> this does not stand for a big additional constraint for the user. >>>>>>> >>>>>>> => The Rserve runnable (server app.) comes with the said R >>>>>>> package >>>>>>> >>>>>>> >>>>>>> Note: I believe we could even simplify the "startMZmine" workflow >>>>>>> , by first trying to detect the R location automatically. >>>>>>> (the environment variables to be assigned in the script >>>>>>> would be used only as a fallback in case the detection failed) >>>>>>> >>>>>>> That would more or less look like (See: >>>>>>> RUtilities.java >>>>>>> ) : >>>>>>> >>>>>>> public static String getRexecutablePath() { >>>>>>> >>>>>>> String osname = >>>>>>> System.getProperty("os.name"); >>>>>>> if (osname != null && osname.length() >>>>>>> >= 7 && osname.substring(0,7).equals("Windows")) { >>>>>>> LOG.log(Level.INFO, "Windows: >>>>>>> query registry to find where R is installed ..."); >>>>>>> String installPath = null; >>>>>>> try { >>>>>>> Process rp = >>>>>>> Runtime.getRuntime().exec("reg query HKLM\\Software\\R-core\\R"); >>>>>>> StreamHog regHog = new >>>>>>> StreamHog(rp.getInputStream(), true); >>>>>>> rp.waitFor(); >>>>>>> regHog.join(); >>>>>>> installPath = >>>>>>> regHog.getInstallPath(); >>>>>>> } catch (Exception rge) { >>>>>>> LOG.log(Level.SEVERE, >>>>>>> "ERROR: unable to run REG to find the location of R: "+rge); >>>>>>> return null; >>>>>>> } >>>>>>> if (installPath == null) { >>>>>>> LOG.log(Level.SEVERE, >>>>>>> "ERROR: canot find path to R. Make sure reg is available and R was >>>>>>> installed with registry settings."); >>>>>>> return null; >>>>>>> } >>>>>>> return installPath + " >>>>>>> \\bin\\R.exe >>>>>>> "; >>>>>>> } >>>>>>> >>>>>>> File f = new >>>>>>> File("/Library/Frameworks/R.framework/Resources/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/usr/local/lib/R/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/usr/lib/R/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/sw/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/usr/common/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> f = new File("/opt/bin/R"); >>>>>>> if (f.exists()) return f.getPath(); >>>>>>> >>>>>>> >>>>>>> return null; >>>>>>> >>>>>>> } >>>>>>> >>>>>>> >>>>>>> * The way it works: >>>>>>> ---------------- >>>>>>> >>>>>>> Rserve is a server (implements a communication protocol with R) >>>>>>> and, to keep it simple, it should be run on localhost and default >>>>>>> port 6311 (this is something that should probably be mentioned >>>>>>> to the user, for >>>>>>> security and eventually firewall configuration reasons >>>>>>> ). >>>>>>> Each time we create a new "RConnection", the main instance of >>>>>>> Rserve starts a new child process. >>>>>>> - We can store the PID of this instance for later termination. >>>>>>> - We can run asynchronously as many instances as we want (as >>>>>>> long as we take care to close/terminate the ones that are no longer >>>>>>> used). >>>>>>> >>>>>>> => I already implemented a basic wrapper (that should be >>>>>>> enhanced) for those operations: >>>>>>> >>>>>>> https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/src/main/java/net/sf/mzmine/util/RSession.java >>>>>>> >>>>>>> (Simplified version of the class in attachment). >>>>>>> >>>>>>> => The code for starting Rserve main server instance is located >>>>>>> in "RUtilities.java" for now: >>>>>>> >>>>>>> https://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/src/main/java/net/sf/mzmine/util/RUtilities.java >>>>>>> >>>>>>> >>>>>>> => >>>>>>> USAGE (a sample use case can be found in the BaselineCorrectionTask.java >>>>>>> ): >>>>>>> >>>>>>> Basically, evaluating one or more R commands is done as >>>>>>> follows: >>>>>>> >>>>>>> - Create and open a new session: >>>>>>> // (This will automatically start >>>>>>> Rserve, if not already running, and open a new slave instance for this >>>>>>> task) >>>>>>> String[] reqPackages = new String[] { >>>>>>> "ptw" }; >>>>>>> RSession rSession = new >>>>>>> RSession(reqPackages); >>>>>>> rSession.open(); >>>>>>> >>>>>>> - Check the additional packages necessary to >>>>>>> perform the commands for the given session: >>>>>>> // Returns the first failing required >>>>>>> package name or null if successful >>>>>>> String missingPackage = >>>>>>> rSession.loadRequiredPackages(); >>>>>>> >>>>>>> - Do some R evaluations, such as: >>>>>>> // Set chromatogram. >>>>>>> >>>>>>> rSession.assignDoubleArray("chromatogram", chromatogram); >>>>>>> // Calculate baseline. >>>>>>> rSession.eval("baseline <- >>>>>>> asysm(chromatogram," + smoothing + "," + asymmetry + ")"); >>>>>>> baseline = >>>>>>> rSession.collectDoubleArray("baseline"); >>>>>>> >>>>>>> - Release the session (closes the socket >>>>>>> connection for the session and ends the related Rserve slave process): >>>>>>> rSession.close(false); >>>>>>> >>>>>>> >>>>>>> Note: >>>>>>> We should also check, at some point, if no more tasks are requiring >>>>>>> Rserve, and shutdown the server. >>>>>>> (it will be restarted the next >>>>>>> time we use a MZmine feature requiring R anyway...) >>>>>>> >>>>>>> * Performance considerations: >>>>>>> -------------------------- >>>>>>> >>>>>>> <Mail Attachment.png> >>>>>>> Source: >>>>>>> http://www.sciencedomain.org/download.php?f=Satman4152014BJMCS10902_1.pdf&aid=4838&type=a >>>>>>> The performances where good enough for what I had to do with the >>>>>>> BaselineCorretors. So, at very first sight, this should fit the other >>>>>>> needs >>>>>>> (anyway, the other very few multi-threaded alternatives I gave a test >>>>>>> where not exploitable in term of evaluation speed). >>>>>>> May be we should/will have to consider switching between JRIengine and >>>>>>> Rserve for some particular features). >>>>>>> I hope not >>>>>>> , but in any case, >>>>>>> this is something which seems doable: as far as I tested, there is >>>>>>> absolutely no incompatibilities between Rserve and JRI. >>>>>>> >>>>>>> To make your own opinion on all this, the BaselineCorretorModule >>>>>>> (again) allows to choose the R engine among >>>>>>> RCaller (Online), JRIengine and Rserve >>>>>>> . >>>>>>> Just run the MZmine version linked on top of this email, and go to "Raw >>>>>>> data methods > Filtering > Baseline Correction" >>>>>>> >>>>>>> <Mail Attachment.png> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Fill free to ask if something is unclear or if you have any further >>>>>>> questionings. >>>>>>> Looking forward to your constructive comments and thoughts... >>>>>>> >>>>>>> I'll be glad to help, as much as possible, with migrating to Rserve (if >>>>>>> it turns out that this solution really is viable). >>>>>>> >>>>>>> Cheers >>>>>>> Gauthier >>>>>>> >>>>>>> >>>>>>> >>>>>>> -------- Forwarded Message -------- >>>>>>> Subject: Re: [Mzmine-devel] Baseline correction >>>>>>> Date: Tue, 2 Dec 2014 05:15:41 +0000 >>>>>>> From: Tomas Pluskal <plus...@oist.jp> >>>>>>> To: Gauthier Boaglio <gauthier.boag...@gmail.com> >>>>>>> >>>>>>> Hi Gauthier, >>>>>>> >>>>>>> Now that we released version 2.12, I think it is a good time to >>>>>>> consider making the switch from JRI to RServe. >>>>>>> I think it is a good idea - I don't really like the current JRI >>>>>>> interface. >>>>>>> >>>>>>> It would be great if you could send a message to the devel list, where >>>>>>> you can summarize what you found about RServe. Especially, we would >>>>>>> like to know >>>>>>> 1) is the initial setup and configuration going to be easier than the >>>>>>> current one (is it necessary to edit the startMZmine script in order to >>>>>>> use RServe?) >>>>>>> 2) how does the actual code differ between RServe and JRI? >>>>>>> >>>>>>> Thanks a lot! >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Tomas >>>>>>> >>>>>>> =============================================== >>>>>>> Tomas Pluskal >>>>>>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate >>>>>>> University >>>>>>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan >>>>>>> WWW: https://groups.oist.jp/g0 >>>>>>> TEL: +81-98-966-8684 >>>>>>> Fax: +81-98-966-2890 >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Gauthier BOAGLIO >>>>>>> CEFE - UMR 5175 >>>>>>> 1919 route de Mende >>>>>>> F-34293 Montpellier cedex 5 >>>>>>> >>>>>>> Tel: +33/0 4 67 61 32 15 >>>>>>> Fax: +33/0 4 67 61 33 36 >>>>>>> >>>>>>> email: >>>>>>> gauthier.boag...@cefe.cnrs.fr >>>>>>> >>>>>>> www: >>>>>>> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio >>>>>>> >>>>>>> >>>>>>> http://www.evolepid.org/people.php?name=boaglio >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> Gauthier BOAGLIO >>>>>> CEFE - UMR 5175 >>>>>> 1919 route de Mende >>>>>> F-34293 Montpellier cedex 5 >>>>>> >>>>>> Tel: +33/0 4 67 61 32 15 >>>>>> Fax: +33/0 4 67 61 33 36 >>>>>> >>>>>> email: >>>>>> gauthier.boag...@cefe.cnrs.fr >>>>>> >>>>>> www: >>>>>> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio >>>>>> >>>>>> >>>>>> http://www.evolepid.org/people.php?name=boaglio >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >>>>>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >>>>>> with Interactivity, Sharing, Native Excel Exports, App Integration & more >>>>>> Get technology previously reserved for billion-dollar corporations, FREE >>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk_______________________________________________ >>>>>> Mzmine-devel mailing list >>>>>> Mzmine-devel@lists.sourceforge.net >>>>>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel >>>>> =============================================== >>>>> Tomas Pluskal >>>>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate >>>>> University >>>>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan >>>>> WWW: https://groups.oist.jp/g0 >>>>> TEL: +81-98-966-8684 >>>>> Fax: +81-98-966-2890 >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >>>>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >>>>> with Interactivity, Sharing, Native Excel Exports, App Integration & more >>>>> Get technology previously reserved for billion-dollar corporations, FREE >>>>> >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk >>>>> >>>>> >>>>> _______________________________________________ >>>>> Mzmine-devel mailing list >>>>> >>>>> Mzmine-devel@lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel >>>> >>>> -- >>>> Gauthier BOAGLIO >>>> CEFE - UMR 5175 >>>> 1919 route de Mende >>>> F-34293 Montpellier cedex 5 >>>> >>>> Tel: +33/0 4 67 61 32 15 >>>> Fax: +33/0 4 67 61 33 36 >>>> >>>> email: >>>> gauthier.boag...@cefe.cnrs.fr >>>> >>>> www: >>>> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio >>>> >>>> >>>> http://www.evolepid.org/people.php?name=boaglio >>>> >>>> >>>> >>>> >>>> >>> =============================================== >>> Tomas Pluskal >>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate >>> University >>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan >>> WWW: https://groups.oist.jp/g0 >>> TEL: +81-98-966-8684 >>> Fax: +81-98-966-2890 >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >>> with Interactivity, Sharing, Native Excel Exports, App Integration & more >>> Get technology previously reserved for billion-dollar corporations, FREE >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk >>> >>> >>> _______________________________________________ >>> Mzmine-devel mailing list >>> >>> Mzmine-devel@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/mzmine-devel >> >> -- >> Gauthier BOAGLIO >> CEFE - UMR 5175 >> 1919 route de Mende >> F-34293 Montpellier cedex 5 >> >> Tel: +33/0 4 67 61 32 15 >> Fax: +33/0 4 67 61 33 36 >> >> email: >> gauthier.boag...@cefe.cnrs.fr >> >> www: >> http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio >> >> >> http://www.evolepid.org/people.php?name=boaglio >> >> >> >> ------------------------------------------------------------------------------ >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >> with Interactivity, Sharing, Native Excel Exports, App Integration & more >> Get technology previously reserved for billion-dollar corporations, FREE >> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk_______________________________________________ >> Mzmine-devel mailing list >> Mzmine-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mzmine-devel > =============================================== > Tomas Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > WWW: https://groups.oist.jp/g0 > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel -- Gauthier BOAGLIO CEFE - UMR 5175 1919 route de Mende F-34293 Montpellier cedex 5 Tel: +33/0 4 67 61 32 15 Fax: +33/0 4 67 61 33 36 email: gauthier.boag...@cefe.cnrs.fr www: http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio http://www.evolepid.org/people.php?name=boaglio ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
