Question

AnnBuilder failing Taffy examples

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Barry Henderson ▴ 250

@barry-henderson-49

Last seen 10.2 years ago

This is a multi-part message in MIME format. ------_=_NextPart_001_01C22E95.ABCD839B Content-Type: multipart/alternative; boundary="----_=_NextPart_002_01C22E95.ABCD839B" ------_=_NextPart_002_01C22E95.ABCD839B Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I have been working on getting AnnBuilder functional without much success. I have a postgresql db running on the system (linux), I have created a devDB. And ABRnwCheck("devDB") exits without errors. =20 But, ... as I work through the Taffy example in the docs I receive the following error with acc2LLMapper: =20 =20 Error in "names<-.default"(*tmp*, value =3D c(byID, id)): Names attribute must be the same length as the vector =20 =20 Any ideas? =20 Thanks =20 Barry =20 =20 =20 =20 Barry S. Henderson, Ph.D. Senior Scientist Ribonomics, Inc. barry.henderson@ribonomics.com =20 =20 <http: www.ribonomics.com=""/>=20 =20 =20 =20 ------_=_NextPart_002_01C22E95.ABCD839B Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable <html xmlns:v="3D" urn:schemas-microsoft-com:vml""="=" ""="" xmlns:o="3D" urn:schemas-microsoft-com:office:office""="=" ""="" xmlns:w="3D" urn:schemas-microsoft-com:office:word""="=" ""="" xmlns="3D" <a="" href="<a href=" http:="" www.w3.org="" TR="" REC-html40"="" rel="nofollow">http://www.w3.org/TR/REC-html40" rel="nofollow">http://www.w3.org/TR/REC-html40""> <head> <meta http-equiv="3DContent-Type" content="3D" text="" html;"="=" ""="" charset="3Dus-ascii" "=""> <meta name="3DProgId" content="3DWord.Document"> <meta name="3DGenerator" content="3D" Microsoft"="" word="" 10"=""> <meta name="3DOriginator" content="3D" Microsoft"="" word="" 10"=""> <link rel="3DFile-List" href="3D" cid:filelist.xml@01C22E74.24A71950""=""> <link rel="3DEdit-Time-Data" href="3D" cid:editdata.mso@01C22E74.24A71950""=""> <style> </style> </head> <body lang="3DEN-US" link="3Dblue" vlink="3Dpurple" =="" style="3D'tab-interval:.5in'">

I have been working on getting AnnBuilder functional without much success. = I have a postgresql db running on the system = (linux), I have created a devDB. And ABRnwCheck(“devDB”) exits without = errors.<o:p></o:p>

<o:p> </o:p>

But, = … as I work through the Taffy example in the docs I receive the following error with acc2LLMapper:<o:p></o:p>

<o:p> </o:p>

Error in “names<-.default”(*tmp*, value =3D c(byID, id)):<o:p></o:p>

Names attribute must be the same length as the = vector<o:p></o:p>

<o:p> </o:p>

Any = ideas?<o:p></o:p></p=>

<o:p> </o:p>

Thanks<o:p></o:p>

<o:p> </o:p>

Barry<o:p></o:p>

<o:p> </o:p>

Barry S. Henderson, = Ph.D.
Senior Scientist
Ribonomics, Inc.
barry.henderson@ribonom ics= .com
<o:p></o:p>

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ADD COMMENT • link 22.4 years ago Barry Henderson ▴ 250

score 0 · Answer 1 · 2002-07-18

Sorry for the HTML.. I have been working on getting AnnBuilder functional without much success. I have a postgresql db running on the system (linux), I have created a devDB. And ABRnwCheck("devDB") exits without errors. But, ... as I work through the Taffy example in the docs I receive the following error with acc2LLMapper: Error in "names<-.default"(*tmp*, value = c(byID, id)): Names attribute must be the same length as the vector Any ideas? Thanks Barry Barry S. Henderson, Ph.D. Senior Scientist Ribonomics, Inc. barry.henderson@ribonomics.com

score 0 · Answer 2 · 2002-07-18

>X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 >content-class: urn:content-classes:message >MIME-Version: 1.0 >X-MS-Has-Attach: yes >Thread-Topic: AnnBuilder failing Taffy examples >Thread-Index: AcIulavGeNDq9DE2Q1eajj3R4M10wA== >From: "Barry Henderson" <barry.henderson@ribonomics.com> >To: "BioConductor Mailing List" <bioconductor@stat.math.ethz.ch> >Subject: [BioC] AnnBuilder failing Taffy examples >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.0.11 >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >List-Archive: <http: www.stat.math.ethz.ch="" pipermail="" bioconductor=""/> >Date: Thu, 18 Jul 2002 15:59:48 -0400 > I could not duplicate the error. Did you use all the example files or just followed the steps in the example to process a real data set? Jianhua

score 0 · Answer 3 · 2002-07-18

I followed the examples explicitly in the pdf for AnnBuilder. -----Original Message----- From: John Zhang [mailto:jzhang@jimmy.harvard.edu] Sent: Thursday, July 18, 2002 4:34 PM To: Barry Henderson; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] AnnBuilder failing Taffy examples >X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 >content-class: urn:content-classes:message >MIME-Version: 1.0 >X-MS-Has-Attach: yes >Thread-Topic: AnnBuilder failing Taffy examples >Thread-Index: AcIulavGeNDq9DE2Q1eajj3R4M10wA== >From: "Barry Henderson" <barry.henderson@ribonomics.com> >To: "BioConductor Mailing List" <bioconductor@stat.math.ethz.ch> >Subject: [BioC] AnnBuilder failing Taffy examples >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.0.11 >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >List-Archive: <http: www.stat.math.ethz.ch="" pipermail="" bioconductor=""/> >Date: Thu, 18 Jul 2002 15:59:48 -0400 > I could not duplicate the error. Did you use all the example files or just followed the steps in the example to process a real data set? Jianhua

score 0 · Answer 4 · 2002-07-18

>X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 >content-class: urn:content-classes:message >Subject: RE: [BioC] AnnBuilder failing Taffy examples >MIME-Version: 1.0 >Date: Thu, 18 Jul 2002 16:45:02 -0400 >X-MS-Has-Attach: >X-MS-TNEF-Correlator: >Thread-Topic: [BioC] AnnBuilder failing Taffy examples >Thread-Index: AcIummultcgt+LfHRzqWfOXEcyqrZgAAUNSQ >From: "Barry Henderson" <barry.henderson@ribonomics.com> >To: "John Zhang" <jzhang@jimmy.harvard.edu>, <bioconductor@stat.math.ethz.ch> >Content-Transfer-Encoding: 8bit >X-MIME-Autoconverted: from quoted-printable to 8bit by blaise.dfci.harvard.edu id QAA19127 > >I followed the examples explicitly in the pdf for AnnBuilder. I will have a closer look at the code and let you know what I find. Thanks. > > > >-----Original Message----- >From: John Zhang [mailto:jzhang@jimmy.harvard.edu] >Sent: Thursday, July 18, 2002 4:34 PM >To: Barry Henderson; bioconductor@stat.math.ethz.ch >Subject: Re: [BioC] AnnBuilder failing Taffy examples > > >>X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 >>content-class: urn:content-classes:message >>MIME-Version: 1.0 >>X-MS-Has-Attach: yes >>Thread-Topic: AnnBuilder failing Taffy examples >>Thread-Index: AcIulavGeNDq9DE2Q1eajj3R4M10wA== >>From: "Barry Henderson" <barry.henderson@ribonomics.com> >>To: "BioConductor Mailing List" <bioconductor@stat.math.ethz.ch> >>Subject: [BioC] AnnBuilder failing Taffy examples >>X-BeenThere: bioconductor@stat.math.ethz.ch >>X-Mailman-Version: 2.0.11 >>List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >>List-Post: <mailto:bioconductor@stat.math.ethz.ch> >>List-Subscribe: ><http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, ><mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >>List-Id: The Bioconductor Project Mailing List ><bioconductor.stat.math.ethz.ch> >>List-Unsubscribe: ><http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, ><mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >>List-Archive: <http: www.stat.math.ethz.ch="" pipermail="" bioconductor=""/> >>Date: Thu, 18 Jul 2002 15:59:48 -0400 >> > > >I could not duplicate the error. Did you use all the example files or >just >followed the steps in the example to process a real data set? > >Jianhua >

score 0 · Answer 5 · 2002-07-18

On Thu, Jul 18, 2002 at 03:59:48PM -0400, Barry Henderson wrote: > I have been working on getting AnnBuilder functional without much > success. I have a postgresql db running on the system (linux), I have > created a devDB. And ABRnwCheck("devDB") exits without errors. > > But, ... as I work through the Taffy example in the docs I receive the > following error with acc2LLMapper: > > > Error in "names<-.default"(*tmp*, value = c(byID, id)): > Names attribute must be the same length as the vector > Can you run traceback() at this point so we can see where you are? Also, once you locate that point, you can put in a call to browser (or use debug on the innermost function), this will let you step through the code one line at a time. you can query different objects and hopefully we can find out what the problem is. Also, you didn't say, but what version of R and what version of postgres? thanks, Robert > > Any ideas? > > Thanks > > Barry > > > > > Barry S. Henderson, Ph.D. > Senior Scientist > Ribonomics, Inc. > barry.henderson@ribonomics.com > > > <http: www.ribonomics.com=""/> > > > -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+

score 0 · Answer 6 · 2002-07-18

Version of R is 1.5.0 Version of postgresql 7.2.1-5 I repeated the process and what I obtained with traceback and debug is inserted below. I am still working on walking through debug (new to R) so querying the locals and making sense of it is not trivial. Thanks Barry *************TRACEBACK OUTPUT************** > acc2LLMapper(outName=testUnified, dbName = "devDB", tName = "abtestmap", baseFile = baseF, toMap = toBeMapped, baseCols = c("id", "acc"), byID = "id") Error in "names<-.default"(*tmp*, value = c(byID, id)) : names attribute must be the same length as the vector > traceback() 4: "names<-.default"(*tmp*, value = c(byID, id)) 3: "names<-"(*tmp*, value = c(byID, id)) 2: mergeMaps(fileParser(TEMPFILE, baseFile, parsed[1], parsed[2]), paste("src", counter, sep = "")) 1: acc2LLMapper(outName = testUnified, dbName = "devDB", tName = "abtestmap", baseFile = baseF, toMap = toBeMapped, baseCols = c("id", "acc"), byID = "id") > ***************************Debug output********************** debug(acc2LLMapper) > acc2LLMapper(outName=testUnified, dbName="devDB", tName="abtestmap", + baseFile=baseF, toMap=toBeMapped, baseCols=c("id", "acc"), byID = "id") debugging in: acc2LLMapper(outName = testUnified, dbName = "devDB", tName = "abtestmap", baseFile = baseF, toMap = toBeMapped, baseCols = c("id", "acc"), byID = "id") debug: { require(RPgSQL) || stop("RPgSQL is not available!") merged <- NULL TEMPFILE <- "tempFile" mergeMaps <- function(srcFile, id) { newCol <- as.data.frame(dropDup(srcFile)) names(newCol) <- c(byID, id) merged <<- merge(merged, newCol, by = byID, all = TRUE) } merged <- as.data.frame(dropDup(baseFile)) names(merged) <- baseCols counter <- 1 for (i in toMap) { parsed <- unlist(strsplit(i, "=")) if (!is.na(parsed[2])) mergeMaps(fileParser(TEMPFILE, baseFile, parsed[1], parsed[2]), paste("src", counter, sep = "")) else mergeMaps(parsed[1], paste("src", counter, sep = "")) counter <- counter + 1 unlink(TEMPFILE) } checkCon(dbName) db.write.table(merged, name = tName, no.clobber = FALSE) db.disconnect() authentic <- getAuthenMap(dbName, tName) write.table(x = authentic, file = outName, quote = FALSE, sep = "\t", row.names = FALSE, col.names = FALSE) } Browse[1]> debug: require(RPgSQL) || stop("RPgSQL is not available!") Browse[1]> debug: merged <- NULL Browse[1]> debug: TEMPFILE <- "tempFile" Browse[1]> debug: mergeMaps <- function(srcFile, id) { newCol <- as.data.frame(dropDup(srcFile)) names(newCol) <- c(byID, id) merged <<- merge(merged, newCol, by = byID, all = TRUE) } Browse[1]> debug: merged <- as.data.frame(dropDup(baseFile)) Browse[1]> debug: names(merged) <- baseCols Browse[1]> debug: counter <- 1 Browse[1]> debug: for (i in toMap) { parsed <- unlist(strsplit(i, "=")) if (!is.na(parsed[2])) mergeMaps(fileParser(TEMPFILE, baseFile, parsed[1], parsed[2]), paste("src", counter, sep = "")) else mergeMaps(parsed[1], paste("src", counter, sep = "")) counter <- counter + 1 unlink(TEMPFILE) } Browse[1]> debug: i Browse[1]> debug: parsed <- unlist(strsplit(i, "=")) Browse[1]> debug: if (!is.na(parsed[2])) mergeMaps(fileParser(TEMPFILE, baseFile, parsed[1], parsed[2]), paste("src", counter, sep = "")) else mergeMaps(parsed[1], paste("src", counter, sep = "")) Browse[1]> debug: counter <- counter + 1 Browse[1]> debug: unlink(TEMPFILE) Browse[1]> debug: i Browse[1]> debug: parsed <- unlist(strsplit(i, "=")) Browse[1]> debug: if (!is.na(parsed[2])) mergeMaps(fileParser(TEMPFILE, baseFile, parsed[1], parsed[2]), paste("src", counter, sep = "")) else mergeMaps(parsed[1], paste("src", counter, sep = "")) Browse[1]> Error in "names<-.default"(*tmp*, value = c(byID, id)) : names attribute must be the same length as the vector > -----Original Message----- From: Robert Gentleman [mailto:rgentlem@jimmy.harvard.edu] Sent: Thursday, July 18, 2002 5:08 PM To: Barry Henderson Cc: BioConductor Mailing List Subject: Re: [BioC] AnnBuilder failing Taffy examples On Thu, Jul 18, 2002 at 03:59:48PM -0400, Barry Henderson wrote: > I have been working on getting AnnBuilder functional without much > success. I have a postgresql db running on the system (linux), I have > created a devDB. And ABRnwCheck("devDB") exits without errors. > > But, ... as I work through the Taffy example in the docs I receive the > following error with acc2LLMapper: > > > Error in "names<-.default"(*tmp*, value = c(byID, id)): > Names attribute must be the same length as the vector > Can you run traceback() at this point so we can see where you are? Also, once you locate that point, you can put in a call to browser (or use debug on the innermost function), this will let you step through the code one line at a time. you can query different objects and hopefully we can find out what the problem is. Also, you didn't say, but what version of R and what version of postgres? thanks, Robert > > Any ideas? > > Thanks > > Barry > > > > > Barry S. Henderson, Ph.D. > Senior Scientist > Ribonomics, Inc. > barry.henderson@ribonomics.com > > > <http: www.ribonomics.com=""/> > > > -- +--------------------------------------------------------------------- -- ----+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- -- ----+