[R] Windows: URL associations do not work in scheduled tasks
Hi, I have a script called test.R which contains: browseURL(http://r-project.org;) It works fine when I run it interactively or with R -f test.R when logged in as the user 'biocbuild'. However, if I set up a Scheduled Task to run the script as that same user (with the XML definition below) it outputs the following: Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. browseURL(http://r-project.org;) Error in shell.exec(url) : file association for 'http://r-project.org' not available or invalid Calls: browseURL - shell.exec Execution halted I tried granting the user that the task runs as (biocbuild) the Log On As A Service right (per https://technet.microsoft.com/en-us/library/Cc739424(v=WS.10).aspx) but that did not make a difference. This is on sessionInfo() R version 3.2.2 RC (2015-08-06 r68871) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows Server 2012 x64 (build 9200) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base I note that I do not have the same issue with Windows Server 2008; I am seeing it now in Windows Server 2012. Here is the task definition: ?xml version=1.0 encoding=UTF-16? Task version=1.2 xmlns=http://schemas.microsoft.com/windows/2004/02/mit/task; RegistrationInfo Date2015-08-17T14:03:12.3440388/Date AuthorWINDOWS1\Administrator/Author /RegistrationInfo Triggers / Principals Principal id=Author UserIdWINDOWS1\biocbuild/UserId LogonTypePassword/LogonType RunLevelLeastPrivilege/RunLevel /Principal /Principals Settings MultipleInstancesPolicyIgnoreNew/MultipleInstancesPolicy DisallowStartIfOnBatteriestrue/DisallowStartIfOnBatteries StopIfGoingOnBatteriestrue/StopIfGoingOnBatteries AllowHardTerminatetrue/AllowHardTerminate StartWhenAvailablefalse/StartWhenAvailable RunOnlyIfNetworkAvailablefalse/RunOnlyIfNetworkAvailable IdleSettings StopOnIdleEndtrue/StopOnIdleEnd RestartOnIdlefalse/RestartOnIdle /IdleSettings AllowStartOnDemandtrue/AllowStartOnDemand Enabledtrue/Enabled Hiddenfalse/Hidden RunOnlyIfIdlefalse/RunOnlyIfIdle WakeToRunfalse/WakeToRun ExecutionTimeLimitP3D/ExecutionTimeLimit Priority7/Priority /Settings Actions Context=Author Exec CommandC:\biocbld\bbs-3.2-bioc\R\bin\R.exe/Command Arguments-f test.R gt; out 2gt;amp;1/Arguments WorkingDirectoryc:\biocbld\bbs-3.2-bioc\meat/WorkingDirectory /Exec /Actions /Task Thanks in advance for any help, Dan __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] install.packages umask configuration
Hi, The R-admin manual says: If installing packages on a Unix-alike to be used by other users, ensure that the system umask is set to give sufficient permissions (see also Sys.umask in R). (To a large extent this is unnecessary in recent versions of R, which install packages as if umask = 022.) I want install.packages() to honor my umask which is 002. I can't find a way to do that; is it possible? My goal is for any user in a specific group to be able to update packages installed by any other user in that group. (This is on an Ubuntu machine.) I've also tried setting a recursive acl on $R_HOME/library in which group write permission is always set, but install.packages() does not seem to honor that. (For the record, this question was asked before (https://stat.ethz.ch/pipermail/r-help/2012-August/321839.html) but not answered.) Thanks, Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] install multtest and preprocessCore packages in Bioconductor library
Hi Nguyen, Subject: [R] install multtest and preprocessCore packages in Bioconductor library Date: Wed, 30 Nov 2011 09:57:36 -0800 From: UyenThao Nguyen ungu...@tethysbio.com To: r-help r-help@r-project.org CC: uth.ngu...@ucdavis.edu uth.ngu...@ucdavis.edu Hi All, I've tried to install these multtest and preprocessCore packages in Mac, but kept getting error messages. I tried to load the packages using 2 ways: 1. Installed from BioConductor (sources) 2. And installed from BioConductor (binaries) Both ways, I got these error messages: For preprocessCore: ld: warning: directory '/usr/local/lib' following -L not found ld: library not found for -lgfortran collect2: ld returned 1 exit status make: *** [preprocessCore.so] Error 1 ERROR: compilation failed for package ‘preprocessCore’ * removing ‘/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore’ For multtest: ld: warning: directory '/usr/local/lib' following -L not found ** arch - x86_64 Looks like the error got to do with L drive, which I don't know how to fix it. Please help. Any suggestions will be greatly appreciated. Thank you very much, Nguyen You don't specify what commands you are using to install these packages. Bioconductor recommends installing packages with biocLite(), like so: source(http://bioconductor.org/biocLite.R;) biocLite(c(multtest, preprocessCore)) Please send the output of those commands, as well as the output of sessionInfo() so we can help solve your problem. Thanks Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] install multtest and preprocessCore packages in Bioconductor library
Hi Nguyen, On Wed, Nov 30, 2011 at 12:11 PM, UyenThao Nguyen ungu...@tethysbio.com wrote: Thank you All for your prompt helps. Dear Dan, Before I used source(http://bioconductor.org/biocLite.R;) biocLite(Biobase) # GET BIOCONDUCTOR PACKAGE FROM SOURCE then, I went to Install packages in Rgui pointing to BioConductor to load these packages in. That was why I got the error messages. Now, I added biocLite(c(multtest,preprocessCore)) and saw that the packages were saved in /var/folders/9m/9mgg3bdhHcmLfSBpO7I6CTI/-Tmp-//Rtmpylgrz5/downloaded_packages, which I am not sure where. # biocLite(c(multtest,preprocessCore)) Using R version 2.10.1, biocinstall version 2.5.11. Installing Bioconductor version 2.5 packages: [1] multtest preprocessCore Please wait... trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.10/multtest_2.4.0.tgz' Content type 'application/x-gzip' length 1694933 bytes (1.6 Mb) opened URL == downloaded 1.6 Mb trying URL 'http://www.bioconductor.org/packages/2.5/bioc/bin/macosx/leopard/contrib/2.10/preprocessCore_1.8.0.tgz' Content type 'application/x-gzip' length 235382 bytes (229 Kb) opened URL == downloaded 229 Kb The downloaded packages are in /var/folders/9m/9mgg3bdhHcmLfSBpO7I6CTI/-Tmp-//Rtmpylgrz5/downloaded_packages Then, I did library(multtest) The fact that this produced no error means that multtest is successfully installed. ?multtest No documentation for 'multtest' in specified packages and libraries: you could try '??multtest' To get help, do this: help(package=multtest) I don't know how to load these functions after they were saved? I am not a computer person, so I don't know what to do when things don't work. You have already loaded the package; library(packagename) is the way to do it. This and the help() bit above should get you started. If you have further questions about these specific packages, please post to the bioconductor list, after reading our posting guide. http://bioconductor.org/help/mailing-list/posting-guide/ Thanks, Dan Thanks again, Nguyen On Nov 30, 2011, at 10:09 AM, Dan Tenenbaum wrote: Hi Nguyen, Subject: [R] install multtest and preprocessCore packages in Bioconductor library Date: Wed, 30 Nov 2011 09:57:36 -0800 From: UyenThao Nguyen ungu...@tethysbio.com To: r-help r-help@r-project.org CC: uth.ngu...@ucdavis.edu uth.ngu...@ucdavis.edu Hi All, I've tried to install these multtest and preprocessCore packages in Mac, but kept getting error messages. I tried to load the packages using 2 ways: 1. Installed from BioConductor (sources) 2. And installed from BioConductor (binaries) Both ways, I got these error messages: For preprocessCore: ld: warning: directory '/usr/local/lib' following -L not found ld: library not found for -lgfortran collect2: ld returned 1 exit status make: *** [preprocessCore.so] Error 1 ERROR: compilation failed for package ‘preprocessCore’ * removing ‘/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/2.10/Resources/library/preprocessCore’ For multtest: ld: warning: directory '/usr/local/lib' following -L not found ** arch - x86_64 Looks like the error got to do with L drive, which I don't know how to fix it. Please help. Any suggestions will be greatly appreciated. Thank you very much, Nguyen You don't specify what commands you are using to install these packages. Bioconductor recommends installing packages with biocLite(), like so: source(http://bioconductor.org/biocLite.R;) biocLite(c(multtest, preprocessCore)) Please send the output of those commands, as well as the output of sessionInfo() so we can help solve your problem. Thanks Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [BioC] arch=i386
On Wed, Apr 27, 2011 at 4:46 AM, Stat Consult statconsul...@gmail.com wrote: Dear ALL I want to load HTSanalyzeR, It 's necessary to load igraph package. This time I see this error: library(igraph) library(HTSanalyzeR) Loading required package: GSEABase Loading required package: Biobase Error: package 'Biobase' is not installed for 'arch=i386' I 'll be glade if you help me Can you please post the output of sessionInfo()? Also, how did you install Biobase? Try this: source(http://bioconductor.org/biocLite.R;) biocLite(Biobase) I'm guessing you are running 32-bit windows but it's hard to know what is going on without more information. I verified that I could run library(Biobase) in R 2.12, 2.13, and 2.14 in 32-bit R on Windows. Dan [[alternative HTML version deleted]] ___ Bioconductor mailing list bioconduc...@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sending a null byte to a socket
Sorry to spam the list again, but I was wondering if anyone has a solution to this. It seems that writing nulls to sockets is a pretty common use case, so I would hope there is a way to do this. Thanks. On Wed, Jun 16, 2010 at 12:52 PM, Dan Tenenbaum dtenenb...@systemsbiology.org wrote: Hello, I am trying to write some code in R to communicate over sockets via the STOMP protocol (http://stomp.codehaus.org/Protocol). As you can see, a null byte (ASCII 0) is used as the over signal. I'd like to be able to do something like this: write.socket(socket, CONNECT\nlogin: me\npasscode: pass\n\n\000) However, R does not like it when you put \000 in a string: \000 Error: embedded nul in string: '\0' I thought perhaps that write.socket would automatically send a null byte, but it doesn't appear to. I'm getting similar results with socketConnection() and writeLines(). I thought that writeBin() might be the solution but it gives me: Error in writeBin(n, con) : can only write to a binary connection I'm not clear how to make my socket a binary connection. I am only going to be writing strings, with the exception of these null bytes. Can anyone suggest a method for doing this? Thanks Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sending a null byte to a socket
OK, I figured this out: s - CONNECT\n\n con - socketConnection(port=61613, blocking=F) writeChar(s, con, nchar(s)) r = readLines(con) r [1] CONNECTED session:ID:yourhost.yourdomain.com-49763-1276709732624-4:28 [4] close(con) Thanks Dan On Wed, Jun 16, 2010 at 12:52 PM, Dan Tenenbaum dtenenb...@systemsbiology.org wrote: Hello, I am trying to write some code in R to communicate over sockets via the STOMP protocol (http://stomp.codehaus.org/Protocol). As you can see, a null byte (ASCII 0) is used as the over signal. I'd like to be able to do something like this: write.socket(socket, CONNECT\nlogin: me\npasscode: pass\n\n\000) However, R does not like it when you put \000 in a string: \000 Error: embedded nul in string: '\0' I thought perhaps that write.socket would automatically send a null byte, but it doesn't appear to. I'm getting similar results with socketConnection() and writeLines(). I thought that writeBin() might be the solution but it gives me: Error in writeBin(n, con) : can only write to a binary connection I'm not clear how to make my socket a binary connection. I am only going to be writing strings, with the exception of these null bytes. Can anyone suggest a method for doing this? Thanks Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sending a null byte to a socket
Hello, I am trying to write some code in R to communicate over sockets via the STOMP protocol (http://stomp.codehaus.org/Protocol). As you can see, a null byte (ASCII 0) is used as the over signal. I'd like to be able to do something like this: write.socket(socket, CONNECT\nlogin: me\npasscode: pass\n\n\000) However, R does not like it when you put \000 in a string: \000 Error: embedded nul in string: '\0' I thought perhaps that write.socket would automatically send a null byte, but it doesn't appear to. I'm getting similar results with socketConnection() and writeLines(). I thought that writeBin() might be the solution but it gives me: Error in writeBin(n, con) : can only write to a binary connection I'm not clear how to make my socket a binary connection. I am only going to be writing strings, with the exception of these null bytes. Can anyone suggest a method for doing this? Thanks Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] .Rprofile is being executed twice
Hi, After updating to R 2.7, my .Rprofile executes twice on startup. I confirmed this by putting in the following line: print(starting .Rprofile...) When I start R, I see: [1] starting .Rprofile... [1] starting .Rprofile... This seems like the obverse of the following FAQ: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-did-my-_002eRprofile-stop-working-when-I-updated-R_003f But in my case .Rprofile is working, just working twice as much as it should. Even if there is nothing in my .Rprofile except that print() statement, it still executes twice. What could be causing this? Thanks Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
