http://blog.gmane.org/gmane.comp.lang.r.db hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.lang.r.db/731 <pre>Hello. Does sqlSave support appending to a table with a computed column? In my attempt, RODBC will not allow the append because I have "missing columns in 'data'" If I create a column in my dataframe as a place holder for the computed column in the table and then try to append the data RStudio experiences an unhandled exception and crashes. Thanks for any advice you might have. Mikael [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Mortensen, Mikael - Marketing 2012-05-25T20:52:44 http://comments.gmane.org/gmane.comp.lang.r.db/728 <pre>We are trying to attach R to our ODBC driver via RODBC. Unfortunately we're getting Segmentation faults in odbcConnect (error detailed below). We would like to attach a debugger to whatever process is communicating with UnixODBC/our driver, but are not sure where to start. R itself seems to be a large bash script, ideally we could inject "gdb --args" before the execution of some process in that script to get the desired results. Any guidance is much appreciated. *** caught segfault *** address 0x100000abb, cause 'memory not mapped' Traceback: 1: .Call(C_RODBCDriverConnect, as.character(connection), id, as.integer(believeNRows)) 2: odbcDriverConnect(st, ...) 3: odbcConnect("sql1010odbc") </pre> Christopher A. Simon 2012-05-17T20:06:22 http://comments.gmane.org/gmane.comp.lang.r.db/723 <pre>Getting frustrated using R with MySQL (on Debian Squeeze). I can connect to mySQL database and I can execute simple queries. But, having various difficulties executing queries with multiple statements separated by ";". Set the client.flag to CLIENT_MULTI_STATEMENTS but still having difficulties. Questions: are the RMySQL and RODBC packages really meant just for simple, one line queries? Can anyone point me to where I might learn how to execute more complicated queries with in R? Thanks! Mark _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Mark Moon 2012-05-17T14:59:38 http://comments.gmane.org/gmane.comp.lang.r.db/721 <pre>Hello, when I query a MySQL database using the commands con &lt;- dbConnect(MySQL(), user=dbuser, password=dbpasswd, dbname=dbname, host=dbhost) df &lt;- dbGetQuery(con, sql) I get the following message when a table contains the timestamp type: RS-DBI driver warning: (unrecognized MySQL field type 7 in column 1 imported as character) I googled and found a post on this mailing list from 2006: https://stat.ethz.ch/pipermail/r-sig-db/2006q3/000221.html Obviously this is still not fixed. Are there any plans to do so? Thanks, Andreas R version 2.15.0 (2012-03-30) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_CH.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RMySQL_0.8-0 DBI_0.2-5 _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Andreas Voellenklee 2012-05-09T14:05:20 http://comments.gmane.org/gmane.comp.lang.r.db/711 <pre>Greetings, I'm not sure if this is the right list for this subject so if not please point me there. rpart() and some other R libraries now have model scoring output in PMML through the pmml library. I do some consulting in predictive modeling and often the companies require SQL case statement code or C# or some other language. I know there are things such as the Oracle solution for in database scoring but this is somewhat different in that typically the IT shops will want the scoring code as the deliverable and then run it natively in the data warehouse they have. Most (all?) commercial data mining and modeling packages have SQL as one of the options for scoring code. SAS eMiner for instance can deliver code in several languages. So can Angoss, KXEN, etc. Does anyone know of an equivalent to the pmml library in SQL? Thomas Brandenburger Assistant Professor Department of Mathematics and Statistics South Dakota State University Cell: 605.480.0951 Fax: 605.688.5880 thomas.brandenburger-B3sqeG8WtU+Vc3sceRu5cw&lt; at &gt;public.gmane.org&lt;mailto:thomas.brandenburger-B3sqeG8WtU+Vc3sceRu5cw&lt; at &gt;public.gmane.org&gt; [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Brandenburger, Thomas 2012-04-19T15:11:11 http://comments.gmane.org/gmane.comp.lang.r.db/710 <pre></pre> siddharth arun 2012-04-14T14:58:27 http://comments.gmane.org/gmane.comp.lang.r.db/709 <pre>I understand that reading date time fields through ODBC can be problematic. When reading a table containing several MS Access date time fields, some are correctly read, others are not. In the snippet below, both DateTimeFld1 and DateTimeFld2 are formatted identically within MS Access. When read in through RODBC date times in the first field are truncated to dates, but the second field imports correctly. I have tried this from both MS Access .mdb and .accdb files, and tried both the odbcConnect and odbcConnectAccess2007 functions with the same results. When using odbcConnect, I have specified a dsn created by C:\Windows\SysWOW64\odbcad32.exe driver? Please advise if there may be a solution to reliably handle date time fields from MS Access. Snippet: PK DateTimeFld1 DateTimeFld2 1 41910 2004-04-26 2004-04-27 02:00:00 [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Anthony S Fischbach 2012-03-27T18:50:12 http://comments.gmane.org/gmane.comp.lang.r.db/707 <pre>Can any one tell how can I find return on the CRSP equally-weighted protfolio from a given set of data from CRSP? </pre> siddharth arun 2012-03-26T23:25:45 http://comments.gmane.org/gmane.comp.lang.r.db/706 <pre>I want to forecast using GARCH function. Can any one help how to do it? </pre> siddharth arun 2012-03-26T23:22:37 http://comments.gmane.org/gmane.comp.lang.r.db/702 <pre>Hi there, I'm pretty new to the use of R with a newly created schema SQLite database. I've been looking to the vignettes and to some examples, but I couldn't find a pretty basic task: i.e. inserting a row in a table only if it doesn't exist. if it does, I would either update or do nothing. this is a simple table in my database variation_id name reference_allele validation_status 1 1 rs123 A not_validated 2 2 rs234 C validated 3 3 rs345 T not_validated and this the small test dataframe I'd like to insert data from variants=data.frame(variation_id=c(1,2,3),name=c("rsNN","rsXX", "rs123"), reference_allele=c("A","C","T"), validation_status=c("not_validated","validated","not_validated")) based on SQL commands I was tempted to write something like dbBeginTransaction(db) query &lt;- paste('IF NOT EXISTS (SELECT * FROM variation WHERE name = :name)', 'INSERT INTO "variation"', "VALUES(NULL, :name, :reference_allele, :validation_status);") dbGetPreparedQuery(db, query, bind.data=variants) but I got the error Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near "IF": syntax error) Anyone who could point me on the right direction? thanks very much, Francesco R Under development (unstable) (2012-01-20 r58146) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RSQLite_0.11.1 DBI_0.2-5 loaded via a namespace (and not attached): [1] tools_2.15.0 --------------------------------------------------------------------------------- Francesco Lescai, PhD, EDBT Senior Research Associate in Genome Analysis University College London Faculty of Population Health Sciences Dept. Genes, Development &amp; Disease ICH - Molecular Medicine Unit, GOSgene team 30 Guilford Street WC1N 1EH London UK email: f.lescai-hclig2XLE9Zaa/9Udqfwiw&lt; at &gt;public.gmane.org&lt;mailto:f.lescai-hclig2XLE9Zaa/9Udqfwiw&lt; at &gt;public.gmane.org&gt; phone: +44.(0)207.905.2274 [ext: 2274] -------------------------------------------------------------------------------- [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Lescai, Francesco 2012-03-20T12:28:28 http://comments.gmane.org/gmane.comp.lang.r.db/700 <pre>I've setup RStudio server and pointed it to use an existing R (2.13) installation. ROracle works fine when accessed from R, but the same does not work from RStudio web-interface. Loading required package: DBI Error in .oci.Driver() : ROracle internal error [rociDrvInit, 1, -1] "/etc/rstudio/rserver.conf" has rsession-which-r=/usr/local/R/bin/R rsession-ld-library-path=/u01/app/oracle/product/11.1.0/db_1/lib:/u01/app/oracle/product/11.1.0/db_1 There is an existing path environment variable defined $ env |grep LD_LIB* =/u01/app/oracle/product/11.1.0/db_1/lib:/u01/app/oracle/product/11.1.0/db_1 RStudio web-interface was giving me the above mentioned issue. I added the path in rserver.conf and restarted the RStudio server but the problem still exists. [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Sai Munikuntla 2012-03-15T15:31:35 http://comments.gmane.org/gmane.comp.lang.r.db/698 <pre>Hello. This is a copy of my email to r-sig-deb I'm trying install roracle in my debian 64 bit system. I've read the http://cran.r-project.org/web/packages/ROracle/INSTALL and I've installed Oracel Instant Client by rpm package (using alien to deb convert). When I try to install I write export LD_LIBRARY_PATH=/usr/lib/oracle/11.2/client64/lib:$LD_LIBRARY_PATH in terminal and then I download ROracle_1.1-1.tar.gz from cran and I type sudo R CMD INSTALL ROracle_1.1-1.tar.gz where I've downloaded the tar.gz file. I always get the same error jose&lt; at &gt;jose-laptop:~/Descargas$ sudo R CMD INSTALL ROracle_1.1-1.tar.gz * installing to library '/usr/local/lib/R/site-library' * installing *source* package 'ROracle' ... ** package 'ROracle' successfully unpacked and MD5 sums checked configure: error: OCI libraries not found ERROR: configuration failed for package 'ROracle' * removing '/usr/local/lib/R/site-library/ROracle' and I don't understand why. any idea? Thanks. [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> jose luis cañadas 2012-03-06T21:27:22 http://comments.gmane.org/gmane.comp.lang.r.db/697 <pre>Hi, I've encountered a snag when trying to create a dataframe from FileMaker data. For what it's woth, I'm uising FileMaker Pro 11, FileMaker's ODBC driver, and ODBC Administrator on MacOS Lion. I am able to sucessfully make the connection. Thus, executes and gives no error messages. However, gives a list of all of the label names of the table (53 in all), but without the variables. confirms this: The editor labels the columns correctly, but the cells are empty. Is this expected behavior, or a bug? Have I overlooked something? Any and all help appreciated! Thank you, </pre> Rolf Marvin Bøe Lindgren 2012-02-23T22:02:11 http://comments.gmane.org/gmane.comp.lang.r.db/696 <pre>Dear R-users, I have to read data from a worksheet that is available on the Internet. I have been doing this by copying the worksheet from the browser. But I would like to be able to copy the data automatically using the url command. But when using "url" command the result is the source code, I mean, a html code. I see that the data I need is in the source code but before thinking about reading the data from the html code I wonder if there is a package or anoher way to extract these data since reading from the code will demand many work and it can be not so accurate. Below one can see the from where I am trying to export the data: dados&lt;-url(" http://www.mar.mil.br/dhn/chm/meteo/prev/dados/pnboia/sc1201_arquivos/sheet002.htm","r ") I am looking forward any help. Thanks in advance , Nilza Barros [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Nilza BARROS 2012-02-12T00:49:07 http://comments.gmane.org/gmane.comp.lang.r.db/693 <pre>Dear R Users and Experts, I got a MySQL table with German special characters (umlaute like ä,ö,ü etc.) . The MySQL database table is in the UTF8 format, and if I submit a query over the MySql client the umlaute are displayed correctly. If I submit the same query via R the umlaute are displayed wrong. That is a little confusing for me, R as well as the MySQL support UTF8. Is there any option which I should use to get the umlaute in R correct? Thanks, Henri \xd6sterreichische Schilling ... _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Henri Mone 2012-02-08T18:24:38 http://comments.gmane.org/gmane.comp.lang.r.db/691 <pre>Hi, I am curious as how to connect to an informix database. I believe this to be possible from what I found but have absolutely no idea how to. If somebody could point me in the right direction please let me know. I posted this on the nabble forum and got no response. Thank you, Scott [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Scott Randall 2012-01-25T22:20:20 http://comments.gmane.org/gmane.comp.lang.r.db/687 <pre>Hi, First, my apologies for a lengthy email. I have been trying to get connectivity between R and Oracle over the past few days (I am new to R, but know Oracle and Linux). I have tried both RODBC and ROracle methods to connect, but having issues with both. Below is our environment, what I have done, and the issues to date. I would much appreciate any help on this, as I'm not sure what to do now. Our server: - RHEL 5.7 64-bit - Oracle 11.2.0.3 64-bit - R version 2.14.0 (2011-10-31) 64-bit i.e. .Machine$sizeof.pointer = 8. _RODBC_ I have installed unixODBC-2.2.14, as I had issues with the standard RHEL 2.2.11. Also installed is the following Oracle 11.2.0.3 64-bit instant client software: - instantclient-basic-linux.x64-11.2.0.3.0 - instantclient-odbc-linux.x64-11.2.0.3.0 - instantclient-precomp-linux.x64-11.2.0.3.0 - instantclient-sdk-linux.x64-11.2.0.3.0 - instantclient-sqlplus-linux.x64-11.2.0.3.0 With the unixODBC 2.2.11 rpm, I kept getting the error with isql: isql: symbol lookup error: /u04/app/oracle/product/11.2.0.3/dbhome_1/lib/libsqora.so.11.1: undefined symbol: SQLGetPrivateProfileStringW This was due to unixODBC 2.2.12+ not being certified on RHEL5 (see attachment bug_12691067.txt for details). After installing the 2.2.14 unixODBC, I can now connect to the local Oracle database with isql. So,... now I do the following as 'root': root&lt; at &gt;predict: export LD_LIBRARY_PATH=/opt/oracle-instantclient/P root&lt; at &gt;predict: export ORACLE_HOME=/u04/app/oracle/product/11.2.0.3/dbhome_1 root&lt; at &gt;predict: export ORACLE_SID=PREDICT root&lt; at &gt;predict: export PATH=/u04/app/oracle/product/11.2.0.3/dbhome_1:/u04/app/oracle/product/11.2.0.3/dbhome_1/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin root&lt; at &gt;predict: export TNS_ADMIN=/u04/app/oracle/product/11.2.0.3/dbhome_1/network/admin root&lt; at &gt;predict:/u05/db_downloads&gt; R R version 2.14.0 (2011-10-31) ... ... ... &gt; &gt; Sys.getenv("ORACLE_SID") [1] "PREDICT" &gt; Sys.getenv("ORACLE_HOME") [1] "/u04/app/oracle/product/11.2.0.3/dbhome_1" &gt; Sys.getenv("LD_LIBRARY_PATH") [1] "/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib:/opt/oracle-instantclient/P:/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib" &gt; Sys.getenv("TNS_ADMIN") [1] "/u04/app/oracle/product/11.2.0.3/dbhome_1/network/admin" &gt; library(RODBC) &gt; hdl &lt;- odbcConnect('predict', '&lt;user&gt;', '&lt;password&gt;') /usr/lib64/R/bin/exec/R: symbol lookup error: /opt/oracle-instantclient/P/libsqora.so.11.1: undefined symbol: SQLGetPrivateProfileStringW root&lt; at &gt;predict:/u05/db_downloads&gt; I noticed the LD_LIBRARY_PATH had my instant client directory appended to it, so I tried updating to be at the start, but I still get the same error. i.e. set to: &gt; Sys.setenv(LD_LIBRARY_PATH="/opt/oracle-instantclient/P:/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib") I find it strange that isql works, but ROracle gives the same error as though I'm running on the unixODBC 2.2.11. Is there something else I need to configure in R to fix this? _ROracle_ I now turn to trying to install the ROracle package, but am unable to get that to install. I have looked at this posting: http://www.mail-archive.com/r-help-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org/msg121901.html ... and the ROracle install package at http://cran.r-project.org/web/packages/ROracle/INSTALL root&lt; at &gt;predict:/u05/db_downloads&gt; R CMD INSTALL ROracle_0.5-12.tar.gz * installing to library '/usr/lib64/R/library' * installing *source* package 'ROracle' ... ** package 'ROracle' successfully unpacked and MD5 sums checked checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/Makefile ** libs ** arch - R CMD COMPILE RS-DBI.c make[1]: Entering directory `/tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/src' gcc -m64 -std=gnu99 -I/usr/include/R -DRS_ORA_SQLGLS_WORKAROUND -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RS-DBI.c -o RS-DBI.o make[1]: Leaving directory `/tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/src' proc CODE=ANSI_C MODE=ORACLE INCLUDE=/usr/lib64/R/include \ PARSE=NONE LINES=false PREFETCH=1 RS-Oracle.pc Pro*C/C++: Release 11.2.0.3.0 - Production on Wed Dec 21 13:59:21 2011 Copyright (c) 1982, 2011, Oracle and/or its affiliates. All rights reserved. System default option values taken from: /u04/app/oracle/product/11.2.0.3/dbhome_1/precomp/admin/pcscfg.cfg R CMD COMPILE RS-Oracle.c make[1]: Entering directory `/tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/src' gcc -m64 -std=gnu99 -I/usr/include/R -DRS_ORA_SQLGLS_WORKAROUND -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RS-Oracle.c -o RS-Oracle.o RS-Oracle.c: In function 'RS_Ora_varCharCpy': RS-Oracle.c:6726: warning: pointer targets in passing argument 1 of '__builtin___strcpy_chk' differ in signedness RS-Oracle.c:6726: warning: pointer targets in passing argument 1 of '__strcpy_ichk' differ in signedness RS-Oracle.c: At top level: RS-Oracle.c:114: warning: 'sqlstm' defined but not used make[1]: Leaving directory `/tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/src' R CMD SHLIB -o ROracle.so RS-DBI.o RS-Oracle.o make[1]: Entering directory `/tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/src' gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o ROracle.so RS-DBI.o RS-Oracle.o -L/u04/app/oracle/product/11.2.0.3/dbhome_1/lib -L/u04/app/oracle/product/11.2.0.3/dbhome_1/network/lib -lclntst11 -lnbeq11 -lnhost11 -lnus11 -lnldap11 -lldapclnt11 -lnsslb11 -lntcp11 -lntcps11 -lnsslb11 -lntcp11 -lntns11 -ldl -lm -lpthread -lnsl -lirc -lipgo -lsvml -ldl -lm -L/usr/lib64/R/lib -lR make[1]: Leaving directory `/tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/src' installing to /usr/lib64/R/library/ROracle/libs ** R ** inst ** preparing package for lazy loading Creating a generic function for 'format' from package 'base' in package 'ROracle' ** help *** installing help indices converting help for package 'ROracle' finding HTML links ... done DBIPreparedStatement-class html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/DBIPreparedStatement-class.Rd:17: missing file link 'dbPrepareStatement' OraConnection-class html OraDriver-class html OraObject-class html OraPreparedStatement-class html OraResult-class html Oracle html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:90: missing file link 'dbRollback' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:99: missing file link 'dbRollback' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:102: missing file link 'dbGetQuery' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:106: missing file link 'dbWriteTable' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:128: missing file link 'dbUnloadDriver' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:133: missing file link 'dbDisconnect' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:139: missing file link 'dbGetQuery' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:140: missing file link 'dbClearResult' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:147: missing file link 'dbRollback' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:154: missing file link 'dbListFields' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:155: missing file link 'dbListConnections' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:156: missing file link 'dbListResults' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:157: missing file link 'dbGetException' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:158: missing file link 'dbGetStatement' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:159: missing file link 'dbHasCompleted' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:160: missing file link 'dbGetRowCount' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/Oracle.Rd:161: missing file link 'dbGetRowsAffected' S4R html dbCallProc-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbCallProc-methods.Rd:30: missing file link 'dbGetQuery' dbCommit-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbCommit-methods.Rd:31: missing file link 'dbGetQuery' dbConnect-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbConnect-methods.Rd:51: missing file link 'dbGetQuery' dbDataType-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbDataType-methods.Rd:32: missing file link 'isSQLKeyword' dbDriver-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbDriver-methods.Rd:38: missing file link 'dbGetQuery' dbGetInfo-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbGetInfo-methods.Rd:47: missing file link 'dbGetQuery' dbListTables-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbListTables-methods.Rd:36: missing file link 'dbColumnInfo' dbObjectId-class html dbPrepareStatement-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbPrepareStatement-methods.Rd:86: missing file link 'dbClearResult' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbPrepareStatement-methods.Rd:87: missing file link 'dbGetStatement' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbPrepareStatement-methods.Rd:88: missing file link 'dbGetRowsAffected' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbPrepareStatement-methods.Rd:109: missing file link 'dbGetQuery' dbReadTable-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbReadTable-methods.Rd:80: missing file link 'dbGetQuery' dbSendQuery-methods html dbSetDataMappings-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/dbSetDataMappings-methods.Rd:34: missing file link 'dbColumnInfo' fetch-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/fetch-methods.Rd:44: missing file link 'dbGetQuery' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/fetch-methods.Rd:45: missing file link 'dbClearResult' isIdCurrent html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/isIdCurrent.Rd:34: missing file link 'dbGetQuery' make.db.names-methods html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/make.db.names-methods.Rd:67: missing file link 'dbWriteTable' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/make.db.names-methods.Rd:68: missing file link 'dbExistsTable' Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/make.db.names-methods.Rd:69: missing file link 'dbRemoveTable' oraParseConParams html oraSupport html safe.write html Rd warning: /tmp/Rtmp50pvF6/R.INSTALL6324d87b/ROracle/man/safe.write.Rd:21: missing file link 'oraWriteTable' summary-methods html ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/ROracle/libs/ROracle.so': /usr/lib64/R/library/ROracle/libs/ROracle.so: undefined symbol: sqlprc Error: loading failed Execution halted ERROR: loading failed * removing '/usr/lib64/R/library/ROracle' As mentioned, I've been through the R forums for answers, but still get this error. I am unsure what to do next, and would much appreciate if anyone would provide some help with either the RODBC method or ROracle method to connect to my database. Thanks in advance, Stuart Uren Database Administrator Clinical Trials Research Unit The University of Auckland Auckland, New Zealand Bug 12691067: UNDEFINED SYMBOL "SQLGETPRIVATEPROFILESTRINGW" – WITH UNIXODBC DM 2.2.11 Show Bug Attributes Bug Attributes Type B - Defect Fixed in Product Version - Severity 2 - Severe Loss of Service Product Version 2.2.11 Status 11 - Code Bug (Response/Resolution) Platform 226 - Linux x86-64 Created 24-Jun-2011 Platform Version RED HAT ENTERPRISE LINUX 5 Updated 16-Oct-2011 Base Bug - Database Version N/A Affects Platforms Port-Specific Product Source Oracle Show Related Products Related Products Line Oracle Database Products Family Oracle Database Area Platform specific utilities Product 579 - Oracle ODBC Driver Hdr: 12691067 N/A DM-UNIX 2.2.11 PRODID-579 PORTID-226 Abstract: UNDEFINED SYMBOL "SQLGETPRIVATEPROFILESTRINGW" – WITH UNIXODBC DM 2.2.11 * o + 06/24/11 03:15 am *** PROBLEM DESCRIPTION: ==================== While using ODBC connection on RH Linux 5 resulted in the following error: isql -v MyDsn isql: symbol lookup error: /usr/lib/oracle/10.2.0.4/client/lib/libsqora.so.10.1: undefined symbol: SQLGetPrivateProfileStringW As per the Note: 762206.1, customer tried to upgrade the unixODBC version from 2.2.11 to 2.2.12 but this version of unixODBC is not supported on RH Linux 5.5 They approached RH support who gave the below explanation for their inability to rebuild unixODBC-2.2.12 and ship that with RHEL 5: ========================================================= I have reviewed the case and see that you are requesting that we can rebase our unixODBC package to version 2.2.12. The case owner, Raghu, has already filed a request for feature enhancement (RFE) with our Product Management team and it is being considered. In order to set your expectations appropriately on this request, we have had ongoing talks with Oracle about this specific issue and unfortunately for our customers, we have not gotten very far in getting this issue resolved. To provide some level of transparency, Oracle started to ship a new driver, which they build against unixODBC-2.2.12, instead of the original version that RHEL 5 ships with. We have requested Oracle, as their software is being certified against RHEL 5, to rebuild against our version of unixODBC. Oracle to date has not complied with our request. On the other hand, we cannot simply rebuild unixODBC-2.2.12 and ship that with RHEL 5 as it would break the Application Binary Compatibility (ABI) guarantee that we give our customers. Versions 2.2.11 and 2.2.12 are not binary compatible, therefore, our customers already relying on 2.2.11 would be left with a broken system if we simply upgraded to 2.2.12. So in short, this request to rebase will not be filled in the short-term. My recommendation would be to join our request to Oracle for a build of the driver against the version of unixODBC that is being shipped with RHEL 5. This is the proper way to fix this issue without impacting the entire set of both Red Hat and Oracle customers. ========================================================= This bug is raised to sort out this problem or atleast provide a workaround for the issue. * o + 06/24/11 03:16 am *** + 06/24/11 03:16 am *** (CHG: Comp. Ver-&gt; 11.2.0.2 -&gt; 2.2.11) + 06/26/11 08:58 pm *** (CHG: Sta-&gt;16) + 06/27/11 01:04 am *** + 06/27/11 01:04 am *** (CHG: Sta-&gt;15) + 06/27/11 01:04 am RESPONSE *** + 07/12/11 09:40 pm RESPONSE *** + 07/13/11 05:16 am *** (CHG: Sta-&gt;20) + 07/13/11 05:16 am RESPONSE *** + 07/13/11 09:53 pm RESPONSE *** 1) The version used by customer is unixODBC 2.2.11 and Oracle ODBC driver 11.2. The OS is RHEL 5.5. With this setup, when they try to use Oracle ODBC driver 11.2 with the unixODBC 2.2.11, they get the below error undefined symbol: SQLGetPrivateProfileStringW 2) Yes that is right "SQLGetPrivateProfileStringW" is defined in libodbcinst.so . But its available only from 2.2.12 on-wards only. Due to which they are forced to upgrade their unixODBC from 2.2.11 to 2.2.12 but 2.2.12 is not supported by the OS RHEL 5.5 due to the above said reasons. Now they are in a deadlock situation. They cannot use the existing unixODBC 2.2.11 nor they can upgrade to 2.2.12 3) There is no mix up. This is a known bug filed with us: Bug 6676290: ORACLE ODBC DRIVER DEPENDENT ON UNIXODBC 2.2.12 which is closed as document bug. The purpose of this bug is to get development views on this issue and if it is feasible to give a new build compatible with unixODBC 2.2.11. * o + 07/13/11 09:53 pm *** (CHG: Sta-&gt;15) + 08/12/11 10:35 am *** + 08/12/11 10:35 am RESPONSE *** + 08/24/11 06:53 am RESPONSE *** + 08/25/11 05:56 am RESPONSE *** + 08/26/11 01:32 am RESPONSE *** + 08/26/11 01:33 am *** (CHG: Sta-&gt;20) + 09/12/11 08:58 pm *** (CHG: Sta-&gt;11 Asg-&gt;NEW OWNER) + 09/12/11 08:58 pm *** + 09/13/11 04:19 am *** + 09/13/11 04:19 am *** + 09/13/11 05:01 am *** + 09/13/11 05:01 am *** + 09/14/11 09:23 pm *** + 10/11/11 10:55 pm *** (CHG: Sta-&gt;30) + 10/11/11 10:55 pm *** + 10/16/11 11:00 pm *** (CHG: Sta-&gt;11) + 10/16/11 11:00 pm *** _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Stuart Uren 2011-12-21T01:27:32 http://comments.gmane.org/gmane.comp.lang.r.db/686 <pre>Hi all, I have recently created a new project/package on r-forge, "easydb". http://easydb.r-forge.r-project.org/ In short: - This package provides a simplified interface to SQLite, MS Access and MySQL (on top of RSQLite and RODBC); - Identical interface (= same functions &amp; arguments) for these 3 databases; - Data subsetting style similar to data.frame, with single square brackets myDatabase[ "myTable", row_constrains, col_name ] - Intended to be user friendly; - Similar to what had been done by John Fox and Oswaldo Cruz in their package dfdb-rodbc; - Database connection handled internally; - Some SQL queries handled internally; - Minimal operation log system, to keep track of operations done on a database; - Internally handles SQL's "LAST_INSERT_ID()" for the 3 databases; Limitations: - Not intended to replace DBI and RODBC. Only the most common operations are covered. - Not designed for speed (but rather usability) All functions are documented + I made a vignette too that cover the most important operation. I was considering to release the package on CRAN, to make it more visible to potential users. Nonetheless, I was wondering what could be the opinion of the R/Database community on this package: Could it be beneficial to the R community, especially R beginners? Or will it add confusion to the confusion (Yet another database package, Yet another data subsetting style)? I was also wondering how to make sure that the code always works as it is supposed to work. As far as I know there are no possibilities for automatic tests of RODBC Access and MySQL during package compilation on r-forge and CRAN -- At the moment I run the tests (testthat, ...) on my local Windows / Linux machines. all the best Julien PS: I must admit I am not an R guRu, and neither an SQL pro... But the package has been tested on rather data-intensive applications. _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Julien Moeys 2011-12-06T09:42:49 http://comments.gmane.org/gmane.comp.lang.r.db/685 <pre>Hi all, A new version of RSQLite is available. Details on new features and fixes below. Thanks to Gabor Grothendieck for some useful bug reports and feature suggestions. + seth Version 0.11.0 - Enhance type detection in sqliteDataType (dbDataType). The storage mode of a data.frame column is now used as part of the type detection. Prior to this patch, all vectors with class other than numeric or logical were mapped to a TEXT column. This patch uses the output of storage.mode to map to integer and double vectors to INTEGER and REAL columns, respectively. All other modes are mapped to a TEXT column. - Detection of BLOBs was narrowed slightly. The code now treats only objects with data.class(obj) == "list" as BLOBs. Previously, is.list was used which could return TRUE for lists of various classes. - Fix bug in sqliteImportFile (used by dbWriteTable) that prevented a comment character from being specified for the input file. - Increase compile-time SQLite limits for maximum number of columns in a table to 30000 and maximum number of parameters (?N) in a SELECT to 40000. Use of wide tables is not encouraged. The default values for SQLite are 2000 and 999, respectively. Databases containing tables with more than 2000 columns may not be compatible with versions of SQLite compiled with default settings. - Upgrade to SQLite 3.7.9. -- Seth Falcon | &lt; at &gt;sfalcon | http://userprimary.net/ _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Seth Falcon 2011-12-01T21:52:19 http://comments.gmane.org/gmane.comp.lang.r.db/682 <pre>I am having an issue compiling and installing ROracle. My knowledge of R is very limited so I am looking for any advice on ways I can troubleshoot and/or solve this issue, i.e. logs, commands, patches, etc. My environment is as follows: Operating System - Red Hat Enterprise Linux AS release 4 (Nahant Update 6) Linux atlqtfldplz01 2.6.9-78.0.1.ELhugemem #1 SMP Tue Jul 22 18:23:25 EDT 2008 i686 i686 i386 GNU/Linux R version 2.14.0 (2011-10-31) Platform: i686-pc-linux-gnu (32-bit) Trying to install ROracle_0.5-12.tar.gz Oracle Client: 10.1.0.3.0 (32bit) ORACLE_HOME=/mass/oracle/product/10.1.0.3.0 LD_LIBRARY_PATH=/mass/oracle/product/10.1.0.3.0/lib Installed R libraries: # /mass/bin/R --slave -e 'cat(rownames(installed.packages()), "\n")' base bitops boot caTools chron class cluster codetools corpcor datasets DBI digest ellipse fAssets fBasics fCopulae fda fields foreign fPortfolio gdata getopt glpk gplots graphics grDevices grid gtools Hmisc KernSmooth lars lattice leaps limSolve lpSolve MASS Matrix methods mgcv mnormt nlme nnet optparse pls proto quadprog Rcpp Rglpk rjson R.methodsS3 robustbase R.oo ROracle roxygen rpart Runiversal slam sn spam spatial splines stats stats4 survival tcltk timeDate timeSeries tools tseries urca utils zoo When attempting to compile/install ROracle I receive the following: # /mass/R/R-2.14.0/bin/R CMD INSTALL -l /mass/R/R-2.14.0/lib/R/library ./ROracle_0.5-12.tar.gz * installing *source* package 'ROracle' ... ** package 'ROracle' successfully unpacked and MD5 sums checked checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E ## You are not building with distcc and have been limited to -j2 ## If you are on the build machine consider stopping and running ## envy distcc before restarting the build configure: creating ./config.status config.status: creating src/Makevars sed: file ./confstatSv9983/subs-1.sed line 43: unterminated `s' command config.status: creating src/Makefile sed: file ./confstatSv9983/subs-1.sed line 43: unterminated `s' command ** libs ** arch - make: *** No targets. Stop. ERROR: compilation failed for package 'ROracle' * removing '/mass/R/R-2.14.0/lib/R/library/ROracle' Has anyone experienced this issue? I haven't found much in the way of documentation out there. Just install procedures, which I've checked and double checked. Not really sure how to troubleshoot this further. Any help will be greatly appreciated. Thanks, -Brad ---------------------------------------------------------------------- This message w/attachments (message) is intended solely ...{{dropped:7}} _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Bowling, Brad 2011-11-14T23:12:31 http://comments.gmane.org/gmane.comp.lang.r.db/679 <pre>Dear all, I have two problems while using R and PostgreSQL 9.0 and need some help. 1) I want to import tables from a specific PostgreSQL-Database into R. Connecting R to PostgreSQL using dbConnect worked, but instead of showing just the tables in the requested database, R returned every single table from all databases. I used these commands: conRLP &lt;- dbConnect(pgSQL(), user = "postgres", password = "pw”, dbname = "Data RLP") dbListTables(conRLP) and now instead of just the 15 tables from “Data RLP” I need, I see a list of all tables. Is there a way to just show the tables that are in Data RLP? My session info: R version 2.13.2 (2011-09-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252 LC_NUMERIC=C LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base 2) I tried to install RPostgreSQL, but got an error report that the confirmation failed. install.packages("RPostgreSQL", type="source") Installiere Paket(e) nach ‘C:/Users/Hinata/Documents/R/win-library/2.13’ #translation from german: install packages to C:/… (da ‘lib’ nicht spezifiziert) #‘lib‘ not specified versuche URL 'http://cran.rakanu.com/src/contrib/RPostgreSQL_0.2-0.tar.gz' #tries URL ´http://…´ Content type 'application/x-gzip' length 159167 bytes (155 Kb) URL geöffnet #URL opened downloaded 155 Kb * installing *source* package 'RPostgreSQL' ... ERROR: configuration failed for package 'RPostgreSQL' * removing 'C:/Users/Hinata/Documents/R/win-library/2.13/RPostgreSQL' Die heruntergeladenen Pakete sind in #downloaded packages can be found in folder c:\users… ‘C:\Users\Hinata\AppData\Local\Temp\RtmpBsQJ05\downloaded_packages’ What can I do? Cheers, Meike [[alternative HTML version deleted]] _______________________________________________ R-sig-DB mailing list -- R Special Interest Group R-sig-DB-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-db </pre> Meike Börder 2011-11-10T10:51:33 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.db