tibco® enterprise runtime for r release notes -...

TIBCO® Enterprise Runtime for R Release NotesSoftware Release 2.5April 2014

Two-Second Advantage®

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TIBCO® Enterprise Runtime for R Release Notes

Contents

TIBCO Enterprise Runtime for R Documentation and Support Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4Prerequisite Information and Installation Detail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5Get Help with TIBCO Enterprise Runtime for R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6TIBCO Enterprise Runtime for R Version 2.5 Release Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

TIBCO Enterprise Runtime for R 2.5 New Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

TIBCO Enterprise Runtime for R 2.5 Additional Enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

TIBCO Enterprise Runtime for R 2.5 R Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

TIBCO Enterprise Runtime for R 2.5 Changes in Functionality Features and Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Closed Issues for TIBCO Enterprise Runtime for R 2.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Known Issues for TIBCO Enterprise Runtime for R 2.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

TIBCO Enterprise Runtime for R version 2.1 Release Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14TIBCO Enterprise Runtime for R 2.1 R Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

TIBCO Enterprise Runtime for R 2.1 Changes in Functionality, Features, and Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Closed Issues in TIBCO Enterprise Runtime for R 2.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Known Issues in TIBCO Enterprise Runtime for R 2.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

TIBCO Enterprise Runtime for R version 2.0 Release Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19TIBCO Enterprise Runtime for R 2.0 New Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

TIBCO Enterprise Runtime for R 2.0 Additional Enhancements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

TIBCO Enterprise Runtime for R 2.0 R Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

TIBCO Enterprise Runtime for R 2.0 Changes in Functionality, Features, and Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Closed Issues in TIBCO Enterprise Runtime for R 2.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Known Issues in TIBCO Enterprise Runtime for R 2.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

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TIBCO Enterprise Runtime for R Documentation andSupport Services

All TIBCO documentation is available in the TIBCO Documentation Library, which can be found here:

https://docs.tibco.com

TIBCO Enterprise Runtime for R Documentation

The following documents for this product can be found in the TIBCO Documentation Library:

● TIBCO® Enterprise Runtime for R Release Notes● TIBCO® Enterprise Runtime for R Technical Guide● TIBCO® Enterprise Runtime for R Java with terrJava● TIBCO® Enterprise Runtime for R Language Reference● Differences Between TIBCO® Enterprise Runtime for R and Open-Source R● TIBCO® Enterprise Runtime for R License Agreement

Product System Requirements

For a list of system requirements for this product and other TIBCO Spotfire® products, visit this site:

http://support.spotfire.com/sr.asp

How to Contact TIBCO Support

For comments or problems with this manual or the software it addresses, contact TIBCO Support asfollows:

● For an overview of TIBCO Support, and information about getting started with TIBCO Support,visit this site:

http://www.tibco.com/services/support

● If you already have a valid maintenance or support contract, visit this site:

https://support.tibco.com

Entry to this site requires a user name and password. If you do not have a user name, you canrequest one.

How to Join TIBCOmmunity

TIBCOmmunity is an online destination for TIBCO customers, partners, and resident experts. It is aplace to share and access the collective experience of the TIBCO community. TIBCOmmunity offersforums, blogs, and access to a variety of resources. To register, go to:

http://www.tibcommunity.com

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https://docs.tibco.com


http://www.tibco.com/services/support


http://www.tibcommunity.com

Prerequisite Information and Installation DetailBefore you install TIBCO® Enterprise Runtime for R, read through the system requirements, supportedplatform information, and guidance on installing and uninstalling.

Supported Platforms, System Requirments, and Installation

For a list of supported platforms and system requirements, see http://support.spotfire.com/sr.asp.

Install and Uninstall on Microsoft Windows

Install: Double-click the file TERR_Console_2.5_win_x86.exe and follow the prompts.

Uninstall: From the Start menu, open Control Panel > Programs > Programs and Features. From theUninstall or change a program list, find and double-click TERR. Follow the instructions in theresulting dialog.

Install and Uninstall on Linux

Install:

1. Unpack the downloaded archive.

2. Change directory into the unpacked directory.

3. Run ./INSTALL and follow the prompts.

Uninstall: Delete the directory created during installation.

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Get Help with TIBCO Enterprise Runtime for RHelp is available for TIBCO® Enterprise Runtime for R from within the console, and from the TIBCOdocumentation website.

To view the TIBCO Enterprise Runtime for R landing page and to get general information about TIBCOEnterprise Runtime for R , and to get a list of included packages and their function help, at the consolecommand line, type help.start(). The landing page is displayed in your browser.

To get more information about batch processing, internationalization, memory management, and othertechnical issues, see the PDF TIBCO Enterprise Runtime for R Technical Guide, available from the TIBCOEnterprise Runtime for R landing page (displayed in your browser when you type help.start() fromthe TIBCO Enterprise Runtime for R console command line).

To get help for a specific function inTIBCO Enterprise Runtime for R , from the console command line,type ?<functionname>, where <functionname> is the name of the function for which you need help.

To get help for managing packages using TIBCO Enterprise Runtime for R , TIBCO Spotfire®, TIBCOSpotfire® Server, and TIBCO Spotfire® Statistics Services, see the PDF TIBCO Enterprise Runtime for R :Package Management, available from the landing page of Spotfire Statistics Services, and from https://docs.tibco.com/products/tibco-enterprise-runtime-for-r.

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https://docs.tibco.com/products/tibco-enterprise-runtime-for-r

https://docs.tibco.com/products/tibco-enterprise-runtime-for-r

TIBCO Enterprise Runtime for R Version 2.5 Release NotesThe Release Notes for this product version are provided to inform you of new features, known issues,and issues from previous releases that have been closed.

These release notes are for TIBCO® Enterprise Runtime for R, April 2014. They cover Linux® andMicrosoft Windows® installations.

TIBCO Enterprise Runtime for R is a high-performance statistical engine, which is compatible withopen-source R. It can be embedded into a wide range of applications as an enterprise-grade alternativeto open-source R, and can run a wide array of packages from CRAN.

Open-source R is available under separate open source software license terms and is not part of TIBCOEnterprise Runtime for R. As such, open-source R is not within the scope of your license for TIBCOEnterprise Runtime for R. Open-source R is not supported, maintained, or warranted in any way byTIBCO Software Inc. Download and use of open-source R is solely at your own discretion and subjectto the free open source license terms applicable to open-source R.

General Improvements

This release of TIBCO Enterprise Runtime for R focuses on supporting improvements to the predictivemodeling and the data function experiences in TIBCO Spotfire®, and to supporting Spotfire dataconnectors. Additional changes include improvements to compatibility with core open-source R andCRAN packages and support for debugging in RStudio.

TIBCO Enterprise Runtime for R 2.5 New PackagesTIBCO® Enterprise Runtime for R provides no new packages in the version 2.5 release.

TIBCO Enterprise Runtime for R 2.5 Additional EnhancementsTIBCO® Enterprise Runtime for R provides additional enhancements in the version 2.5 release.

Enhancement Description

TIBCO Enterprise Runtime for Rsupport to the RStudio IDE.

TIBCO Enterprise Runtime for R supports debuggingfunctionality using the RStudio IDE (www.RStudio.com),including the following:

● Interactive breakpoint setting in a script window toexecute a function and break execution at a specifiedline.

● At any breakpoint, display the current call stack(traceback) and values of all variables in the currentframe.

● At any breakpoint, either step forward to the next lineof execution, or continue execution to the nextsucceeding breakpoint.

● At any breakpoint, modify the values contained in thecurrent frame using standard R commands at thecommand prompt.

For more information about using RStudio with TIBCOEnterprise Runtime for R, see the README for this feature,available from the TIBCO Enterprise Runtime for R launchpage.

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Provided API for Spotfire dataconnections.

TIBCO Enterprise Runtime for R includes functions in theSpotfireData package, including sdcConnect, sdcGetInfo,and sdcGetData to support connecting to, gatheringinformation about, and getting data from the data sourcesavailable through the Spotfire Connectors.

Support for debugging. The functions trace and browser provide support fordebugging from the command line in TIBCO EnterpriseRuntime for R.

Additional support for Spotfirepredictive modeling.

Variable importance support was added to help supportnew predictive modeling features in Spotfire.

Improved compatibility with open-source R and CRAN packages.

See TIBCO Enterprise Runtime for R 2.5 R Compatibility

Upgraded OpenSSL. TIBCO Enterprise Runtime for R uses the OpenSSL libraryprimarily for supporting HTTPS connections. This libraryhas been updated to version 1.0.1g.

TIBCO Enterprise Runtime for R 2.5 R CompatibilityWith every release of TIBCO® Enterprise Runtime for R, we test for compatibility with open-source Rand provide detailed information about differences.

We tested against open-source R version 3.0.2 for this release.

This release includes greater compatibility with the following core R functions and CRAN packages,based on customer feedback.

Compatibility improved for the following CRAN packages:

● bnlearn package

● boot package

● cluster package

● earth package

● gRain package

● MASS package

● Matrix package

● mgcv package

● penalized package

Compatibility either provided or improved for the following functions:

● browser function

● fix function

● dendrogram functions

● hist function

● regmatches function

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● smooth.spline function

● system.time functions

● trace function

● withVisible function

For more information:

● For summary information about the differences between TIBCO Enterprise Runtime for R andopen-source R, from the TIBCO Enterprise Runtime for R console, type help.start(), and in theresulting landing page, click the link Differences Between TIBCO Enterprise Runtime for R and Open-Source R.

● For a complete list of non-statistics functions not included in this release, see the FAQ Base andUtilities Functions and Methods Not Available in TIBCO Enterprise Runtime for R 2.5 at https://support.tibco.com, or at the TIBCO Enterprise Runtime for R community site at https://www.tibcommunity.com/community/products/analytics/terr.

TIBCO tests only the examples provided with CRAN packages for compatibility. For a list of CRANpackages whose examples have been successfully tested, see the FAQ CRAN Packages Compatible withTIBCO Enterprise Runtime for R at https://support.tibco.com.

TIBCO does not warrant, deliver, or support code or other material provided by the R Project forStatistical Computing, including but not limited to development tools and packages, and such code andother material does not constitute a part of TIBCO Enterprise Runtime for R.

TIBCO Enterprise Runtime for R 2.5 Changes in Functionality Features andCompatibility

From TIBCO® Enterprise Runtime for R release to release, we might change the functionality,deprecate, or remove features. In cases where product changes require migration procedures, weprovide information for that purpose.

Changes in Functionality

This release of TIBCO Enterprise Runtime for R contains no changes in functionality.

Migration and Compatibility

This release of TIBCO Enterprise Runtime for R requires no migration procedures and has nocompatibility issues.

Closed Issues for TIBCO Enterprise Runtime for R 2.5The list of closed issues in TIBCO® Enterprise Runtime for R 2.5.

Key Issue

TERR-1773 If you used the where argument with the trace function, the argument wouldfail. The function trace now is fully implemented and this behavior is fixed.

TERR-2803 Returning an invisible value from inside a loop did not work. This has beenfixed.

TERR-2957 Calling getOption("defaultPackages") now returns TIBCO EnterpriseRuntime for R default packages (not including "base").

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https://www.tibcommunity.com/community/products/analytics/terr



Key Issue

TERR-3182 It was not possible to save a connection in TIBCO Enterprise Runtime for R . Thisproblem has been fixed.

TERR-4340 Calling the treeClassFit() function in the SpotfireStats package could throw afactor error. This problem has been fixed.

TERR-4535 RStudio did not install the rstudio and manipulate packages when starting withTIBCO Enterprise Runtime for R . This problem has been fixed, and the packagesnow load when RStudio starts.

TERR-4542 If an NA existed in the predictor for logisticRegFit, you would get an error.This problem has been fixed.

TERR-4560 Running a parallel operation on a big data object could cause TIBCO EnterpriseRuntime for R to fail with a Java OutOfMemory error. This issue has beenaddressed, and the error is handled appropriately.

TERR-4575 TIBCO Enterprise Runtime for R required the MSVCR100 dll to start. Thisproblem has been fixed.

TERR-4576 The clusterExport function in the parallel package ran slowly on some Linuxcomputers. This problem has been fixed.

TERR-4582 RStudio error handler would fail with an error. This problem is fixed.

TERR-4585 Setting the TERR_HOME environment variable caused instability if you usedTIBCO Enterprise Runtime for R with RStudio.

TERR-4607 The assignment operator <- failed if its replacement had the length zero. Thisproblem has been fixed.

TERR-4608 Setting the heap size for the JVM when using the terrJava package on Windowsdid not increase the heap size as expected. This problem has been fixed on theWindows 64-bit platform, but the Windows 32-bit platform limits the heap sizeto 800M.

TERR-4661 TIBCO Enterprise Runtime for R would run slower than open-source R whenrunning certain recursive examples. This problem has been fixed.

TERR-4675 calling tryCatch(readRDS(), error=) would change warnings to errors. Thisproblem has been fixed.

TERR-4677 Serialization problems with TIBCO Enterprise Runtime for R would causeproblems with certain objects created in open-source R. This problem has beenfixed.

TERR-4701 The functions seq.int and rep_len() returned attributes in TIBCO EnterpriseRuntime for R but not in open-source R. This issue has been corrected.

TERR-4704 Printing a function object now usess the R-compatible srcref attribute info toprint the source information.

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Key Issue

TERR-4712 The validate function would fail if it was unable to create a text file called temp.This problem has been fixed.

TERR-4717 the histSmo function in the gamlss package was failing because it did not havethe mids compontent from hist. This has been corrected.

TERR-4719 In TIBCO Enterprise Runtime for R , calling rnorm(5,3,0) resulted in a vector of5 0s, rather than a vector of 5 3s, as it does in open-source R. This problem hasbeen fixed.

TERR-4723 The open-source R function approxfun now works in TIBCO Enterprise Runtimefor R .

TERR-4724 Calling help() and specifying an HTML help type on a function in a packagestored in open-source R's library directory would result in a File Not Found errorin the browser. This problem has been fixed.

TERR-4726 The stats package could not import using the getFunction method if themethods library was not in the search path. This problem has been fixed.

TERR-4728 TIBCO Enterprise Runtime for R would sometimes fail due to a problem withcleaning up the environments before running garbage collection. This problemhas been fixed.

TERR-4730 Adding dim attributes to a factor allowed matrix subsetting to work in open-source R, but not in TIBCO Enterprise Runtime for R . This problem has beenfixed.

TERR-4736 Printing certain expressions in TIBCO Enterprise Runtime for R caused theirsrcfile attribute to be printed, unlike in open-source R. This problem has beenfixed.

TERR-4751 When running TIBCO Enterprise Runtime for R in RStudio, the architectureenvironment variable was not set, as it was in open-source R. This problem hasbeen fixed.

TERR-4752 The function format.factor did not pass the dim and dimnames attributes of afactor as its output. This problem has been fixed.

TERR-4754 When TIBCO Enterprise Runtime for R ran with RStudio, neitherTERRprofile.site nor ~/.TERRprofile were loaded on startup. This problem hasbeen fixed.

TERR-4766 When running TERR RHOME, the home directory of TIBCO Enterprise Runtime forR should be printed to stdout, and then exit. Instead, it would start TIBCOEnterprise Runtime for R with a warning. This problem has been fixed.

TERR-4769 In TIBCO Enterprise Runtime for R , the function unlist did not dispatch to S3methods. This problem has been fixed.

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Key Issue

TERR-4773 The function factor[] <- newValue failed if there were no subscripts in thesubscript list. This problem has been fixed.

TERR-4789 When TIBCO Enterprise Runtime for R ran under TIBCO Spotfire® StatisticsServices, the Java API would give an error because the XML with the responsevalue contained illegal XML 1.0 characters. This problem has been fixed.

TERR-4798 Because predict.glm called the generic summary function rather, rather thancalling summary.glm, it resulted in an error when calling predict.gam withse.fit=TRUE. This problem has been fixed.

TERR-4800 It was not possible to create a call object from an expression in TIBCO EnterpriseRuntime for R . This problem has been fixed.

TERR-4810 set.seed(NULL) now sets .Random.seed to a new randomly-selected value.

Known Issues for TIBCO Enterprise Runtime for R 2.5We have provided a description of Known Issues for your information.

In this release, some R functionality is not available, including graphics devices, and some functionsfrom the base and stats packages. Likewise, S4 is not entirely compatible. For more information, see TIBCO Enterprise Runtime for R 2.5 R Compatibility.

Difference in Denormalized Doubles

In open-source R, arithmetic operations can produce small denormalized floating point numbers. InTIBCO Enterprise Runtime for R , they are coerced to 0. For example, in open-source R, .Machine$double.xmin/2 is about 1.112537e-308, but in TIBCO Enterprise Runtime for R , it is 0.('Denormalized' means that the number cannot be stored to full 52-bit precision because the exponentwould overflow, so it is stored to a lesser precision.)

When running on RedHat Linux, TIBCO Enterprise Runtime for R processes spawned by theparallel package may immediately crash

We have seen a problem when running TIBCO Enterprise Runtime for R on RedHat Linux withversions of Java earlier than 1.7.0_40. If you call the makeCluster function in the parallel package tospawn new TIBCO Enterprise Runtime for R processes, these processes may immediately crash with afatal Java error. To test if this problem is occurring, try the following:library(parallel)c1 <- makeCluster(1, outfile="")# create cluster with one spawned process# specifying outfile="" to print all outputc1 <- makeCluster(1, outfile="")clusterEvalQ(c1, 123)

If this problem is occurring, you will see an error such as the following:> library(parallel)> # create cluster with one spawned process> # specifying outfile="" to print all output from the process> c1 <- makeCluster(1, outfile="")Creating 1 TERR cluster nodes at Thu Oct 24 15:39:39 2013 > clusterEvalQ(c1, 123)1: #1: # A fatal error has been detected by the Java Runtime Environment:1: #1: # SIGSEGV (0xb) at pc=0x0000003ac2cbbfa5, pid=12649, tid=10750549121: #

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1: # JRE version: 7.0_13-b201: # Java VM: Java HotSpot(TM) 64-Bit Server VM (23.7-b01 mixed mode linux-amd64 compressed oops)1: # Problematic frame:1: # C [libstdc++.so.6+0xbbfa5) __cxa_allocate_exception+0x551: #1: # Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again1: #1: # An error report file with more information is saved as:1: # /a/seafiler01.na.tibco.com/vol/vol2/users/sannella/hs_err_pid12649.log1: #1: # If you would like to submit a bug report, please visit:1: # http://bugreport.sun.com/bugreport/crash.jsp1: #Error in waitForClusterReady(cl) : some cluster nodes have crashed or stopped: all crashed

The workaround for this problem is to set the LD_PRELOAD environment variable to libstdc++.so.6.This can be done before TIBCO Enterprise Runtime for R is started, or within TIBCO EnterpriseRuntime for R , before the parallel library has been loaded:> Sys.setenv("LD_PRELOAD"="libstdc++.so.6")> library(parallel)Loading required package: terrJava> c1 <- makeCluster(1, outfile="")Creating 1 TERR cluster nodes at Thu Oct 24 15:47:00 2013 > # create cluster with one spawned process> # specifying outfile="" to print all output> c1 <- makeCluster(1, outfile="")Creating 1 TERR cluster nodes at Thu Oct 24 15:47:00 2013 > clusterEvalQ(c1, 123)1: TIBCO Software Inc. Confidential Information1: Copyright (C) 2011-2013 TIBCO Software Inc. ALL RIGHTS RESERVED1: TIBCO Enterprise Runtime for R version 2.0.0 for Linux 64-bit1: 1: Type 'help()' for help.1: Type 'q()' to quit.1: started engine node pid==12828 at Thu Oct 24 15:47:04 2013[[1]][1] 123>

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TIBCO Enterprise Runtime for R version 2.1 Release NotesThe Release Notes for this product version are provided to inform you of new features, known issues,and issues from previous releases that have been closed.

These release notes are for TIBCO® Enterprise Runtime for R, February 2014. They cover Linux® andMicrosoft Windows® installations.



General Improvements

TIBCO Enterprise Runtime for R has improved in its performance, specifically with the functionreturn().The poly.transform function from Spotfire S+ has been added to the SplusUtils package in TIBCOEnterprise Runtime for R . (Calling poly.transform() on the coefficients recovers the simplepolynomial form. )


We tested against open-source R version 3.0.2 for this release.

This release includes greater compatibility with the following packages, based on customer feedback.These include the following:

● boot● class● cluster● e1071● MASS● mboost● mgcv● penalized● prim● randomForest● ridge● rpart● survival

We have also added hierarchical (hclust()) and K-mean (kmeans()) clustering.

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We have made improvements to Spline, making it sufficient to support mgcv gam model creation:

● spline

● splineDesign

We have expanded compatibility with bioconductor packages.

● For summary information about the differences between TIBCO Enterprise Runtime for R andopen-source R, from the TIBCO Enterprise Runtime for R console, type help.start(), and in theresulting landing page, click the link Differences Between TIBCO Enterprise Runtime for R and Open-Source R.

● For a complete list of non-statistics functions not included in this release, see the FAQ Base andUtilities Functions and Methods Not Available in TIBCO Enterprise Runtime for R 2.1 at https://support.tibco.com, or at the TIBCO Enterprise Runtime for R community site at https://www.tibcommunity.com/community/products/analytics/terr.


TIBCO does not warrant, deliver, or support code or other material provided by the R Project forStatistical Computing, including but not limited to development tools and packages, and such code andother material does not constitute a part of TIBCO Enterprise Runtime for R .

TIBCO Enterprise Runtime for R 2.1 Changes in Functionality, Features,and Compatibility






Closed Issues in TIBCO Enterprise Runtime for R 2.1The list of closed issues in TIBCO® Enterprise Runtime for R 2.1.

Key Issue

TERR-694 Column names of a summary were left-justified. They now match open-source Rand are right-justified.

TERR-3753 Comparison between a list and a string in TIBCO Enterprise Runtime for R didnot allow for a comparison between vector-likely data and an empty string. Thisissue has been fixed.

TERR-4521 A call to object.size(structure(item, attr="an attribute") returned 64bytes, no matter how big item was. This issue has been fixed.

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Key Issue

TERR-4533 The call to ?package::function did not open the help for the function in thespecified package as expected. This issue has been corrected.

TERR-4537 The REvaluator objects in the package RinR call ".../R" to start R alwayslaunched the 32-bit version of open-source R on Windows, if it did not call aspecific argument for the 64-bit version. It now launches the version of open-source R that matches the TIBCO Enterprise Runtime for R version that called it.

TERR-4538 The solve() function failed if given the argument tol=NULL. This issue has beenfixed.

TERR-4543 Using na.action=na.arbor in an arbor model with missing values in thepredictor led to a segmentation fault. This issue has been fixed.

TERR-4546 In TIBCO Enterprise Runtime for R , when rbind was given a data.framecontaining a factor column and a matrix containing character data, it produced afactor column with NAs. This did not occur in open-source R. This issue has beenfixed.

TERR-4553 A scoping problem in model.tables.aovlist() caused a problem finding datathat was not global in scope. This issue has been fixed.

TERR-4559 On Windows, after a call to system was interrupted, the on.exit command didnot work. this issue has been fixed.

TERR-4572 In degenerate models (with as many predictors as cases), the TIBCO EnterpriseRuntime for R function anova.lm omitted the Residuals rows and the F-statisticand P-value columns. This is not the case in open-source R. TIBCO EnterpriseRuntime for R has been changed to match the behavior in open-source R.

TERR-4577 The scope argument for add1 could be a fitted model object. This problem hasbeen corrected so that the non-character non-formula scope is converted to aformula.

TERR-4578 A pairlist comparison could be seen to parse incorrectly if a string was not UTF-8encoded. Named comparisons are now done in the UTF-8 encoded versions ofthe strings.

TERR-4579 The function add1.lm was not working correctly with aov objects. This issue hasbeen fixed.

TERR-4580 The function validObject had problems with infinite recursion. This issue hasbeen fixed.

TERR-4581 The RGraph() function in the RinR package was often unsuccessful indetermining which datasets were required to evaluate its expr argument. Thisbehavior has been improved.

TERR-4584 In open-source R, Linux version$os is listed as "linux-gnu" but in TIBCOEnterprise Runtime for R , it was listed as just "linux". They now match.

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Key Issue

TERR-4596 kmeans in TIBCO Enterprise Runtime for R now accepts x as a vector and anumeric data frame.

TERR-4597 TIBCO Enterprise Runtime for R now allows calling the local definition of the ~function.

TERR-4598 rownames default assumed that the array involved had exactly two dimensions.This caused rownames with a one-dimensional array to fail. This issue has beenfixed.

TERR-4599 The TIBCO Enterprise Runtime for R anova.lmlist had a different argumentusage than that found in open-source R. This issue has been fixed.

TERR-4622 The operator || failed when it compared non-vector arguments. This issue hasbeen fixed.

TERR-4626 TERRscript.exe failed when passing an expression or a file. This issue has beenfixed.

TERR-4630 The arguments in strptime() were reversed from those found in open-source R.They now match.

TERR-4656 Calling format() for a data.frame with zero columns caused an error. It nowreturns a zero-column data.frame with the same row names (hence number ofrows) as the input data.frame.

TERR-4658 When a data.frame had zero rows, the drop=TRUE argument to [.data.framehad no effect. This issue has been corrected.

Known Issues in TIBCO Enterprise Runtime for R 2.1We have provided a description of Known Issues for your information.





We have seen a problem when running TIBCO Enterprise Runtime for R on RedHat Linux withversions of Java earlier than 1.7.0_40. If you call the makeCluster function in the parallel package to

17


spawn new TIBCO Enterprise Runtime for R processes, these processes may immediately crash with afatal Java error. To test if this problem is occurring, try the following:library(parallel)c1 <- makeCluster(1, outfile="")# create cluster with one spawned process# specifying outfile="" to print all outputc1 <- makeCluster(1, outfile="")clusterEvalQ(c1, 123)

If this problem is occurring, you will see an error such as the following:> library(parallel)> # create cluster with one spawned process> # specifying outfile="" to print all output from the process> c1 <- makeCluster(1, outfile="")Creating 1 TERR cluster nodes at Thu Oct 24 15:39:39 2013 > clusterEvalQ(c1, 123)1: #1: # A fatal error has been detected by the Java Runtime Environment:1: #1: # SIGSEGV (0xb) at pc=0x0000003ac2cbbfa5, pid=12649, tid=10750549121: #1: # JRE version: 7.0_13-b201: # Java VM: Java HotSpot(TM) 64-Bit Server VM (23.7-b01 mixed mode linux-amd64 compressed oops)1: # Problematic frame:1: # C [libstdc++.so.6+0xbbfa5) __cxa_allocate_exception+0x551: #1: # Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again1: #1: # An error report file with more information is saved as:1: # /a/seafiler01.na.tibco.com/vol/vol2/users/sannella/hs_err_pid12649.log1: #1: # If you would like to submit a bug report, please visit:1: # http://bugreport.sun.com/bugreport/crash.jsp1: #Error in waitForClusterReady(cl) : some cluster nodes have crashed or stopped: all crashed


18


TIBCO Enterprise Runtime for R version 2.0 Release NotesThe Release Notes for this product version are provided to inform you of new features, known issues,and issues from previous releases that have been closed.

These release notes are for TIBCO® Enterprise Runtime for R, November 2013. They cover Linux®, andMicrosoft Windows® installations.



TIBCO Enterprise Runtime for R 2.0 New PackagesTIBCO® Enterprise Runtime for R provides new packages in the version 2.0 release.

Package Name Description

RinR The RinR package provides functions for running code in open-source Rfrom TIBCO Enterprise Runtime for R, or running code in TIBCOEnterprise Runtime for R from open-source R.

Using RinR, you can:

● Compare results of running the same code in different open-source Rand TIBCO Enterprise Runtime for R versions.

● Call a statistics function from an open-source R package and returnthe results to TIBCO Enterprise Runtime for R .

● Generate a graph in open-source R and return a PNG file to open-source R, TIBCO Enterprise Runtime for R, or Spotfire.

parallel The parallel package contains a subset of functions to providecompatibility for open-source R's parallelized computing feature. Usingthe TIBCO Enterprise Runtime for R's parallel package, you can:

● Define and create a cluster of TIBCO Enterprise Runtime for Rcomputation nodes, either locally (multiple cores on a singlemachine) or remotely (on multiple machines running TIBCOSpotfire® Statistics Services).

● Execute a parallelized computation on a cluster using one of a familyof parallelized apply functions.

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TIBCO Enterprise Runtime for R 2.0 Additional EnhancementsTIBCO® Enterprise Runtime for R provides additional enhancements in the version 2.0 release.


Added TIBCO Enterprise Runtime forR support to the RStudio IDE

The RStudio IDE (www.RStudio.com), an open-sourceintegrated development environment for R, now workswith the TIBCO Enterprise Runtime for R engine. For moreinformation, see the README for this feature, availablefrom the TIBCO Enterprise Runtime for R launch page.

Added the TERRscript application. The new executable TERRscript provides scriptingcapability compatible with the open-source R applicationRscript.

Implemented the capabilitiesfunction.

Added for open-source R compatibility. The capabilitiesfunction returns a named logical vector giving the status ofthe specified capabilities.

Improved modelling functions. Added the functions add1 and drop1 to improvemodelling in TIBCO Enterprise Runtime for R .

Implemented the simplify="array"argument to sapply.

Added for R compatibility. If simplify = "array", andthe function being applied returns equal-sized arrays,sapply returns a single array with one more dimension.See the help for sapply for more information.

Improvements to the methodspackage. ● The 'slots' argument has been implemented in the

setClass method. This argument takes a list of stringsor a character vector, specifying the slots for this class.See the help for setClass for more information.

● The .hasSlot function has been added to the methodspackage. .hasSlot detects slots defined in the objectclass, as well as other attributes added to the object.

● The .valueClassTest function has been added to themethods package. The RSQLite package needs thisfunction to work.

Improvements to the iconv()function.

The function iconv() now includes the argument toRaw,which, if set to TRUE, converts the output strings as a list ofraw vectors (and NA strings as NULL values).

Also, iconv now allows a list of raw vectors, and it allowsNULL as input. If the argument x is a list of raw vectors andNULL values, it is interpreted in the same way. Using thisalternative form for representing strings, it is possible tomanipulate strings in "UTF-16" encoding with embeddedzero bytes. See the help for iconv for more information.

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We tested against open-source R version 3.0.2 for this release. For summary information about thedifferences between TIBCO Enterprise Runtime for R and open-source R, from the TIBCO EnterpriseRuntime for R console, type help.start(), and in the resulting landing page, click the link DifferencesBetween TIBCO Enterprise Runtime for R and Open-Source R.

For a complete list of non-statistics functions not included in this release, see the FAQ Base and UtilitiesFunctions and Methods Not Available in TIBCO Enterprise Runtime for R 2.0 at https://support.tibco.com, orat the TIBCO Enterprise Runtime for R community site at https://www.tibcommunity.com/community/products/analytics/terr.


TIBCO does not warrant, deliver, or support code or other material provided by the R Project forStatistical Computing, including but not limited to development tools and packages, and such code andother material does not constitute a part of TIBCO Enterprise Runtime for R .

TIBCO Enterprise Runtime for R 2.0 Changes in Functionality, Features,and Compatibility




Deprecated and Removed Features

TIBCO Enterprise Runtime for R 2.0 no longer supports Microsoft Windows XP®.



Closed Issues in TIBCO Enterprise Runtime for R 2.0The list of closed issues in TIBCO® Enterprise Runtime for R 2.0.

Key Issue

TERR-2185 The TIBCO Enterprise Runtime for R function gsub with the argumentfixed=TRUE and replacement including a backslash did not work. This problemhas been corrected.

TERR-2494 The TIBCO Enterprise Runtime for R function print prints the column names ofa 0-row matrix with the column names as a vector of character strings, precededby a [1] (which should not have been included).

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Key Issue

TERR-3087 The TIBCO Enterprise Runtime for R function sapply did not work on lists orpairlists containing the missing argument flag. sapply has been fixed.

TERR-3173 The TIBCO Enterprise Runtime for R function var.test did not take lm objectsas inputs, whereas open-source R function var.test does. TIBCO EnterpriseRuntime for R now matches open-source R.

TERR-3280 The robust and pcaPP packages failed to load in TIBCO Enterprise Runtime forR . This has been fixed.

TERR-3710 The TIBCO Enterprise Runtime for R function Reduce ignored its initargument. This has been corrected.

TERR-3715 In TIBCO Enterprise Runtime for R , in the sub() and gsub() functions, thecharacter '$' in a replacement was read like "\\". It is now treated an ordinarycharacter.

TERR-3988 In TIBCO Enterprise Runtime for R , the libedit library referred to freed memorywhen TIBCO Enterprise Runtime for R exited. This behavior has been fixed.

TERR-4072 In TIBCO Enterprise Runtime for R , if you called install.packages() to installto a non-writable directory, it would produce errors. It has been changed so itoffers to make and use a new writable library directory in which to place thepackages.

TERR-4084 In TIBCO Enterprise Runtime for R , AIC lacked the k=2 argument, where in thestats package, its two methods default and logLike have the argument. this hasbeen fixed.

TERR-4090 In TIBCO Enterprise Runtime for R , time(1:10) returned an object of class ts,where in open-source R, it returns a numeric. TIBCO Enterprise Runtime for Rhas been changed to behave the same as open-source R.

TERR-4128 In TIBCO Enterprise Runtime for R , the formatC argument preserve.width hasbeen changed to provide correct behavior for the options "individual","common", and "none". (Note that it is used only if big.mark or small.markarguments are supplied.)

TERR-4130 Open-source R's formatC contains the option format="fg", with which it tries toput enough digits after the decimal point to give 'digits' digits of accuracy,gives unlimited accuracy to the left of the decimal point, and never usesexponential notation. TIBCO Enterprise Runtime for R has been changed tomatch this behavior more closely with the following differences:

● Open-source R sometimes adds a space before "NA", while TIBCO EnterpriseRuntime for R does not.

● When using flag="#+", open-source R converts 0 to "0" instead of "+0", asdoes TIBCO Enterprise Runtime for R

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Key Issue

TERR-4134 In open-source R, window(x, start, end)<-newvalues would, with awarning, extend a time series if the start or end dates are outside the range oftime(x). TIBCO Enterprise Runtime for R window<- did not reigster the attemptto extend the time series, and mangled the replacement, with warnings. It hasbeen changed to match open-source R.

TERR-4140 Open-source R's help() function allows the value of the package argument to bean unquoted string so that help(lm, package=stats)[[1]] and help(lm,package="stats")[[1]] produced the same results. In TIBCO EnterpriseRuntime for R , the quoted version did not work. This issue has been fixed.

TERR-4158 Intermittently, TIBCO Enterprise Runtime for R would report an invalidTERR_HOME directory. This issue has been corrected.

TERR-4159 cor(method = "spearman") encountered performance problems in TIBCOEnterprise Runtime for R . These problems have been addressed, and theperformance problems are solved.

TERR-4162 Open-source R 2.15 function complete.cases ignores NULL arguments, whereTIBCO Enterprise Runtime for R does not ignore them, and copies row names ofinput to its output. The TIBCO Enterprise Runtime for R behavior has beenchanged to match that of Open-source R.

TERR-4173 The TIBCO Enterprise Runtime for R function iconv(NA_character_,from="ASCII", to="UTF-8") returned "NA" instead of NA_character_, thuscausing the problem noted in TERR-4174. This issue has been fixed.

TERR-4174 The TIBCO Enterprise Runtime for R function Sys.getenv("noSuchEnvVar",unset=NA_character_) returned "NA" instead of NA_character_. This issue hasbeen fixed with TERR-4173.

TERR-4178 The Open-source R function abbreviate(NA_character_) returnedNA_character, where TIBCO Enterprise Runtime for R returned "NA". TIBCOEnterprise Runtime for R has been changed to match the open-source R behavior.

TERR-4179 The TIBCO Enterprise Runtime for R functions as.hexmode() andas.octmode() threw an error when given an empty string. In open-source R,these functions returned 0, given an empty string. TIBCO Enterprise Runtime forR has been changed to match the open-source R behavior.

TERR-4181 Open-source R 2.15 splines library functions bs() and ns() were changed tospecify knots=NULL, and was treated the same as omitting the knots argument.TIBCO Enterprise Runtime for R was changed to match this behavior.

TERR-4202 When using anova.glm (test="F") for a family with fixed variance, TIBCOEnterprise Runtime for R should produce a warning and use df2=inf whencomputing p-value of an F test.

TERR-4210 TIBCO Enterprise Runtime for R did not stop with an error if HoltWinters datacontained a 0 and the seasonal argument was "multiplicative" and aseasonal term was requested (the default).

23


Key Issue

TERR-4213 TIBCO Enterprise Runtime for R could not load the CRAN package robustbase.

TERR-4302 TIBCO Enterprise Runtime for R would echo input from readLines whenreading from stdin(), even if the option echo=FALSE was set.

TERR-4306 The TIBCO Enterprise Runtime for R function refObjectGenerator now matchesthe version found in open-source R 3.0.

TERR-4341 The TIBCO Enterprise Runtime for R tryCatch(return()) would return theerror "no function to return from" for non-local returns. Now it matchesopen-source R's behavior of allowing non-local returns.

TERR-4368 The function gettextf() would cause the TIBCO Enterprise Runtime for R tohang with certain input.

TERR-4390 The century intuited for 2-digit years for years between 33 and 69 did not matchopen-source R. TIBCO Enterprise Runtime for R has been changed to matchopen-source R.

Known Issues in TIBCO Enterprise Runtime for R 2.0We have provided a description of Known Issues for your information.





We have seen a problem when running TIBCO Enterprise Runtime for R on RedHat Linux withversions of Java earlier than 1.7.0_40. If you call the makeCluster function in the parallel package tospawn new TIBCO Enterprise Runtime for R processes, these processes may immediately crash with afatal Java error. To test if this problem is occurring, try the following:library(parallel)c1 <- makeCluster(1, outfile="")# create cluster with one spawned process# specifying outfile="" to print all outputc1 <- makeCluster(1, outfile="")clusterEvalQ(c1, 123)

If this problem is occurring, you will see an error such as the following:> library(parallel)> # create cluster with one spawned process> # specifying outfile="" to print all output from the process> c1 <- makeCluster(1, outfile="")Creating 1 TERR cluster nodes at Thu Oct 24 15:39:39 2013 > clusterEvalQ(c1, 123)1: #

24


1: # A fatal error has been detected by the Java Runtime Environment:1: #1: # SIGSEGV (0xb) at pc=0x0000003ac2cbbfa5, pid=12649, tid=10750549121: #1: # JRE version: 7.0_13-b201: # Java VM: Java HotSpot(TM) 64-Bit Server VM (23.7-b01 mixed mode linux-amd64 compressed oops)1: # Problematic frame:1: # C [libstdc++.so.6+0xbbfa5) __cxa_allocate_exception+0x551: #1: # Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again1: #1: # An error report file with more information is saved as:1: # /a/seafiler01.na.tibco.com/vol/vol2/users/sannella/hs_err_pid12649.log1: #1: # If you would like to submit a bug report, please visit:1: # http://bugreport.sun.com/bugreport/crash.jsp1: #Error in waitForClusterReady(cl) : some cluster nodes have crashed or stopped: all crashed


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