From vkhur@n@ @end|ng |rom m@||@nm|@@h@w@||@edu Tue Jul 6 23:42:22 2004 From: vkhur@n@ @end|ng |rom m@||@nm|@@h@w@||@edu (Vikram Khurana) Date: Tue, 6 Jul 2004 11:42:22 -1000 Subject: [R-sig-DB] ROracle returning zero rows Message-ID: <005201c463a2$21da6870$d5a410ac@swfc2.nmfs.gov> Hi, I have ROracle 0.5-5 and DBI 0.1-8 installed on RH 7.3 machine trying to access Oracle 8.1.7 Other config: Gcc 2.96 R 1.9.1 patched I can get to Oracle using sqlplus & retrieve the data from the table "test". However when I try doing the same using ROracle I get the following > library("ROracle") > ora = Oracle() > con <-oraNewConnection(ora,username="user",password="pwd", dbname="database SID") > dbGetQuery(con,"select * from test where rownum<9") [1] VESSEL_CODE CRUISE_NUMBER EVENT_YEAR EVENT_MONTH EVENT_DAY [6] MIN_OCTANT MAX_OCTANT <0 rows> (or 0-length row.names) > dbListTables(con) character(0) When I do a dbGetQuery, I get just the column names of the table show up & no data. There are 1000+ rows in this table in the database. When I do a dbListTables, I get no results, which is not true What is the issue here? Am I doing something wrong? I have googled on it & found another person with the same problem, but no solution. Thanks for your time, Vikram From dj @end|ng |rom re@e@rch@be||-|@b@@com Wed Jul 7 14:25:21 2004 From: dj @end|ng |rom re@e@rch@be||-|@b@@com (David James) Date: Wed, 7 Jul 2004 08:25:21 -0400 Subject: [R-sig-DB] ROracle returning zero rows In-Reply-To: <005201c463a2$21da6870$d5a410ac@swfc2.nmfs.gov>; from vkhurana@mail.nmfs.hawaii.edu on Tue, Jul 06, 2004 at 11:42:22AM -1000 References: <005201c463a2$21da6870$d5a410ac@swfc2.nmfs.gov> Message-ID: <20040707082521.A24999@jessie.research.bell-labs.com> Hi Vikram, I've had several reports of the same problem -- all running Oracle 9 from Linux. AFAIK this problem does not occur on other platforms or other Oracle versions. Unfortunately, I my setup is is different. -- David Vikram Khurana wrote: > Hi, > > I have ROracle 0.5-5 and DBI 0.1-8 installed on RH 7.3 machine trying to > access Oracle 8.1.7 > Other config: > Gcc 2.96 > R 1.9.1 patched > > > I can get to Oracle using sqlplus & retrieve the data from the table "test". > However when I try doing the same using ROracle I get the following > > > library("ROracle") > > ora = Oracle() > > con <-oraNewConnection(ora,username="user",password="pwd", > dbname="database SID") > > dbGetQuery(con,"select * from test where rownum<9") > [1] VESSEL_CODE CRUISE_NUMBER EVENT_YEAR EVENT_MONTH EVENT_DAY > [6] MIN_OCTANT MAX_OCTANT > <0 rows> (or 0-length row.names) > > dbListTables(con) > character(0) > > When I do a dbGetQuery, I get just the column names of the table show up & > no data. There are 1000+ rows in this table in the database. > When I do a dbListTables, I get no results, which is not true > > What is the issue here? Am I doing something wrong? > > I have googled on it & found another person with the same problem, but no > solution. > > Thanks for your time, > Vikram > > _______________________________________________ > R-sig-DB mailing list -- R Special Interest Group > R-sig-DB at stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-db From joe@@pe|g|e @end|ng |rom jk|h@u@ Wed Jul 7 17:23:02 2004 From: joe@@pe|g|e @end|ng |rom jk|h@u@ (joseph speigle) Date: Wed, 7 Jul 2004 10:23:02 -0500 Subject: [R-sig-DB] sending patches to maintenair and general installation issues In-Reply-To: ; from r-sig-db-request@stat.math.ethz.ch on Wed, Jul 07, 2004 at 05:52:48PM +0200 References: Message-ID: <20040707102302.C30854@hovey.hoveymotorcars.com> hello list, I am writing about the Rdbi.pgsql package by following this link from personal mail with the sourceforge maintener, thk from users.sourceforge I hope you can help me with the installation. I can't find a makefile in the download from sourceforge. Also, there are no instructions. I downloaded from http://sourceforge.net/projects/rdbi/ . I can run configure but that's it. It substitutes its variables in Makevars but there is no makefile. It doesn't mention linking against the R libraries, or installation instructions like where to put the module, if it's a dynamic module or not. (these may be in the docs but let me finish) Secondly, if I wanted to write up this deficiency and submit patches in the future if and when I start working on the project, what would be the way to do that and who should I contact? Is the project being maintained, and if so, who is primarily in charge? joesp From ro@@|n| @end|ng |rom b||ndg|obe@net Wed Jul 7 18:59:54 2004 From: ro@@|n| @end|ng |rom b||ndg|obe@net (A.J. Rossini) Date: Wed, 07 Jul 2004 09:59:54 -0700 Subject: [R-sig-DB] sending patches to maintenair and general installation issues In-Reply-To: <20040707102302.C30854@hovey.hoveymotorcars.com> (joseph speigle's message of "Wed, 7 Jul 2004 10:23:02 -0500") References: <20040707102302.C30854@hovey.hoveymotorcars.com> Message-ID: <858ydvoir9.fsf@servant.blindglobe.net> For that particular package, I think that we've got an updated version with a few patches available from the Bioconductor project, http://www.bioconductor.org/ since it is used for some of the annotation packages. joseph speigle writes: > hello list, I am writing about the Rdbi.pgsql package by following > this link from personal mail with the sourceforge maintener, thk from > users.sourceforge I hope you can help me with the installation. I > can't find a makefile in the download from sourceforge. Also, there > are no instructions. I downloaded from > http://sourceforge.net/projects/rdbi/ . I can run configure but > that's it. It substitutes its variables in Makevars but there is no > makefile. It doesn't mention linking against the R libraries, or > installation instructions like where to put the module, if it's a > dynamic module or not. (these may be in the docs but let me finish) > Secondly, if I wanted to write up this deficiency and submit patches > in the future if and when I start working on the project, what would > be the way to do that and who should I contact? Is the project being > maintained, and if so, who is primarily in charge? > > joesp > > _______________________________________________ R-sig-DB mailing list > -- R Special Interest Group R-sig-DB at stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-db > -- Anthony Rossini Research Associate Professor rossini at u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}} From j|mmc|ough||n @end|ng |rom e@rth||nk@net Fri Jul 23 19:08:44 2004 From: j|mmc|ough||n @end|ng |rom e@rth||nk@net (Jim McLoughlin) Date: Fri, 23 Jul 2004 10:08:44 -0700 Subject: [R-sig-DB] best way to access PgSQL from R? Message-ID: Hi, I'm having a problem with R.app on OSX, where it crashes when I invoke dbDisconnect(). This may not be a DBI specific problem, but I wanted to make sure I was using the right database packages to try and isolate why R is crashing. From what I've read, DBI does not yet support a PostgresSQL driver, so the latest driver is in the Rdbi and Rdbi.PgSQL modules, correct? This is how I have been accessing PgSQL: library("chron") #needed for date columns library("Rdbi") library("Rdbi.PgSQL") pcon <- dbConnect(PgSQL(),host="localhost",dbname="test",user="postgres",passwor d="") dbListTables(pcon) #works fine, as do other SQL operations dbDisconnect(pcon) #causes R to pause, then crash Can someone confirm whether this is the most up-to-date way to access PostgresSQL databases (I'm running PostgresSQL 7.4.2)? thanks, Jim M From tke|tt @end|ng |rom m@||@utex@@@edu Fri Jul 23 19:38:12 2004 From: tke|tt @end|ng |rom m@||@utex@@@edu (Timothy H. Keitt) Date: Fri, 23 Jul 2004 12:38:12 -0500 Subject: [R-sig-DB] best way to access PgSQL from R? In-Reply-To: References: Message-ID: <1090604292.5324.28.camel@workstation-3> There was a bug in Rdbi.PgSQL that caused a segfault on releasing the connection. The C-code returns NULL instead of SEXP. That's not allowed, but is undocumented (at least at the time). T. On Fri, 2004-07-23 at 12:08, Jim McLoughlin wrote: > Hi, > > I'm having a problem with R.app on OSX, where it crashes when I invoke > dbDisconnect(). This may not be a DBI specific > problem, but I wanted to make sure I was using the right database > packages to try and isolate why R is crashing. > > From what I've read, DBI does not yet support a PostgresSQL driver, so > the latest driver is in the Rdbi and Rdbi.PgSQL modules, correct? > > This is how I have been accessing PgSQL: > > library("chron") #needed for date columns > library("Rdbi") > library("Rdbi.PgSQL") > > pcon <- > dbConnect(PgSQL(),host="localhost",dbname="test",user="postgres",passwor > d="") > > dbListTables(pcon) #works fine, as do other SQL operations > > dbDisconnect(pcon) #causes R to pause, then crash > > Can someone confirm whether this is the most up-to-date way to access > PostgresSQL databases (I'm running PostgresSQL 7.4.2)? > > thanks, > > Jim M > > _______________________________________________ > R-sig-DB mailing list -- R Special Interest Group > R-sig-DB at stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-db -- Timothy H. Keitt Section of Integrative Biology University of Texas at Austin http://www.keittlab.org/ From m@|| @end|ng |rom joeconw@y@com Fri Jul 23 19:57:44 2004 From: m@|| @end|ng |rom joeconw@y@com (Joe Conway) Date: Fri, 23 Jul 2004 10:57:44 -0700 Subject: [R-sig-DB] best way to access PgSQL from R? In-Reply-To: References: Message-ID: <41015198.2010706@joeconway.com> Jim McLoughlin wrote: > From what I've read, DBI does not yet support a PostgresSQL driver, so > the latest driver is in the Rdbi and Rdbi.PgSQL modules, correct? I believe there is a slightly updated version available as part of the Bioconductor project; see: http://www.bioconductor.org/repository/release1.4/package/html/RdbiPgSQL.html Not sure if it solves your particular issue though. HTH, Joe From j|mmc|ough||n @end|ng |rom e@rth||nk@net Fri Jul 23 20:09:20 2004 From: j|mmc|ough||n @end|ng |rom e@rth||nk@net (Jim McLoughlin) Date: Fri, 23 Jul 2004 11:09:20 -0700 Subject: [R-sig-DB] best way to access PgSQL from R? In-Reply-To: <41015198.2010706@joeconway.com> References: <41015198.2010706@joeconway.com> Message-ID: <6B6E1004-DCD3-11D8-A12F-000393B2DF14@earthlink.net> Thanks, this fixed everything. I was previously using the Rdbi and Rdbi.PgSQL packages from sourceforge (version 0.1.2) cheers, Jim On Jul 23, 2004, at 10:57 AM, Joe Conway wrote: > Jim McLoughlin wrote: >> From what I've read, DBI does not yet support a PostgresSQL driver, >> so the latest driver is in the Rdbi and Rdbi.PgSQL modules, correct? > > I believe there is a slightly updated version available as part of the > Bioconductor project; see: > http://www.bioconductor.org/repository/release1.4/package/html/ > RdbiPgSQL.html > > Not sure if it solves your particular issue though. > > HTH, > > Joe >