specifications for exonmap database config file?
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Joseph Fass ▴ 70
@joseph-fass-2739
Last seen 2.9 years ago
I can't find consistent or complete documentation on how to set up a config file for communicating with a local ensembl database using exonmap. The R help page for xmapConnect says that the function uses a file called "databases.txt", and points me to the package installation instructions to find out how to set it up. But the package (exonmap_1.0.07.tar.gz) installation instructions only talk about config files called, for example, "human.mycnf", and refer to example configuration files available at http://xmap.picr.man.ac.uk, which I can't find. In the INSTALL.txt that came with xmap_homo_sapiens_core_50_36l.tgz<http: xmap.picr.man.ac.uk="" downloads="" xmap_homo_sapiens_core_50_36l.tgz="">there is no description of this file format either, though there was a thread here suggesting that. I have a working installation of ensembl's and xmap's human_core_50_36l, and I've made a directory called ".exonmap" under my home directory, and in that directory placed a file called "databases.txt" that looks like this: 'name' 'species' 'db.name' 'type' 'host' 'port' 'username' 'password' 'Human' 'human' 'homo_sapiens_core_50_36l' '?' ' myserver.correctlocation.edu' '3306' 'correctuser' 'correctpasswd' ... with the correct host/user/pwd info ... and it's tab-separated, and those single quotes are really in there (no quotes didn't any differently) ... I tried a file called human.mycnf, but that didn't seem to make xmapConnect happy. I don't know what's really supposed to go in name, species, or type ... I assume name just dictates the argument you later give to xmapConnect, but are species and type critical? Right now, xmapConnect tells me this: > xmapConnect("Human") Error in if (v != "<ask>") { : argument is of length zero Did I entirely miss some set of documentation? -- Joseph Fass Bioinformatics Programmer UC Davis Bioinformatics Core joseph.fass -at- gmail.com (professional) 970.227.5928 (c) || 530.752.2698 (w) [[alternative HTML version deleted]]
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 8.4 years ago
Hi Joseph > I can't find consistent or complete documentation on how to set up a > config > file for communicating with a local ensembl database using exonmap. The R > help page for xmapConnect says that the function uses a file called > "databases.txt", and points me to the package installation instructions to > find out how to set it up. But the package (exonmap_1.0.07.tar.gz) > installation instructions only talk about config files called, for > example, > "human.mycnf", and refer to example configuration files available at > http://xmap.picr.man.ac.uk, which I can't find. First of all, you'll want to update your exonmap package! The current version is something like 2.0.01, and it's undergone fairly extensive changes. One of those changes is how to connect to the database. It used to be via an "human.mycnf" file in earlier versions of exonmap, but this has now been replaced by "databases.txt". An example is given in INSTALL.pdf at http://www.bioconductor.org/packages/2.3/bioc/html/exonmap.html > In the INSTALL.txt that > came with > xmap_homo_sapiens_core_50_36l.tgz<http: xmap.picr.man.ac.uk="" downloa="" ds="" xmap_homo_sapiens_core_50_36l.tgz="">there > is no description of this file format either, though there was a > thread here suggesting that. > > I have a working installation of ensembl's and xmap's human_core_50_36l, > and > I've made a directory called ".exonmap" under my home directory, and in > that > directory placed a file called "databases.txt" that looks like this: > 'name' 'species' 'db.name' 'type' 'host' 'port' > 'username' 'password' > 'Human' 'human' 'homo_sapiens_core_50_36l' '?' ' > myserver.correctlocation.edu' '3306' 'correctuser' > 'correctpasswd' > Close, but I think that you'll have to specify the "type", i.e. "core" or "otherfeatures". I don't have access to my R-related folders at the moment, but I think I have something along the lines of: name species db.name type host port username password "human" "homo_sapiens" "homo_sapiens_core_50_36l" "core" "my-mysql-location" "4094" "heidi" "my-password" > ... with the correct host/user/pwd info ... and it's tab-separated, and > those single quotes are really in there (no quotes didn't any differently) > ... > I tried a file called human.mycnf, but that didn't seem to make > xmapConnect > happy. I don't know what's really supposed to go in name, species, or > type > ... I assume name just dictates the argument you later give to > xmapConnect, > but are species and type critical? > Right now, xmapConnect tells me this: > >> xmapConnect("Human") > Error in if (v != "<ask>") { : argument is of length zero > What does traceback() say? What's your sessionInfo? You might also have to set Sys.setenv(R_XMAP_CONF_DIR="path/.exonmap") depending on the location of your databases.txt file if this isn't already done, although this error message seems to relate to something else. Cheers \Heidi > > Did I entirely miss some set of documentation? > > > -- > Joseph Fass > Bioinformatics Programmer > UC Davis Bioinformatics Core > joseph.fass -at- gmail.com (professional) > 970.227.5928 (c) || 530.752.2698 (w) > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thanks for your amazingly fast reply, Heidi! ... On Mon, Dec 8, 2008 at 2:57 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote: > Hi Joseph > > > I can't find consistent or complete documentation on how to set up a > > config > > file for communicating with a local ensembl database using exonmap. The > R > > help page for xmapConnect says that the function uses a file called > > "databases.txt", and points me to the package installation instructions > to > > find out how to set it up. But the package (exonmap_1.0.07.tar.gz) > > installation instructions only talk about config files called, for > > example, > > "human.mycnf", and refer to example configuration files available at > > http://xmap.picr.man.ac.uk, which I can't find. > > First of all, you'll want to update your exonmap package! The current > version is something like 2.0.01, and it's undergone fairly extensive > changes. One of those changes is how to connect to the database. It used > to be via an "human.mycnf" file in earlier versions of exonmap, but this > has now been replaced by "databases.txt". An example is given in > INSTALL.pdf at > http://www.bioconductor.org/packages/2.3/bioc/html/exonmap.html Yikes! I was looking at an old documentation page <smacks forehead=""> ... but I *do* have exonmap 2.0.0 installed. Thanks for the heads-up. I altered my "databases.txt" file to be: name species db.name type host port username password "Human" "human" "homo_sapiens_core_50_36l" "core" " tao.genomecenter.ucdavis.edu" "" "<ask>" "<ask>" and now: > xmapConnect() Select a database to connect to: 1: Human ('homo_sapiens_core_50_36l') Selection: 1 username:*** password:*** Error in mysqlNewConnection(dbDriver(drv), ...) : Argument client.flag must be an integer value * * ... but the client.flag value is hardcoded into the function, right? ... I was also getting a warning about R_XMAP_CONF_DIR not being set ... I set it and the warning went away, but no change in the above error ... traceback and sessionInfo: > traceback() 9: stop("Argument client.flag must be an integer value") 8: mysqlNewConnection(dbDriver(drv), ...) 7: is(object, Cl) 6: is(object, Cl) 5: .valueClassTest(standardGeneric("dbConnect"), "DBIConnection", "dbConnect") 4: dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = a[5], client.flag = "196608") 3: FUN(newX[, i], ...) 2: apply(dbs, 1, function(a) { port <- a[6] if is.na(port)) { con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = a[5], client.flag = "196608") } else { con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = a[5], port = port, client.flag = "196608") } }) 1: xmapConnect() and ... > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] exonmap_2.0.0 RMySQL_0.7-2 DBI_0.2-4 RColorBrewer_1.0-2 [5] genefilter_1.22.0 survival_2.34-1 affy_1.20.0 Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2 [4] preprocessCore_1.4.0 RSQLite_0.7-1 Thanks again, ~Joe -- Joseph Fass Bioinformatics Programmer UC Davis Bioinformatics Core joseph.fass -at- gmail.com (professional) 970.227.5928 (c) || 530.752.2698 (w) [[alternative HTML version deleted]]
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Just wanted to add that I noticed I had exonmap 2.0.0, ... so I installed 2.0.01, and am seeing the same error: > > xmapConnect() > Select a database to connect to: > > 1: Human ('homo_sapiens_core_50_36l') > > Selection: 1 > username:*** > password:*** > Error in mysqlNewConnection(dbDriver(drv), ...) : > Argument client.flag must be an integer value > -- Joseph Fass Bioinformatics Programmer UC Davis Bioinformatics Core joseph.fass -at- gmail.com (professional) 970.227.5928 (c) || 530.752.2698 (w) [[alternative HTML version deleted]]
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Hi Joseph, quick question; do you get the same error message when you specify which port to use in your databases.txt file? In your first email you used 3306, does that still apply? \Heidi > Just wanted to add that I noticed I had exonmap 2.0.0, ... so I installed > 2.0.01, and am seeing the same error: > > >> > xmapConnect() >> Select a database to connect to: >> >> 1: Human ('homo_sapiens_core_50_36l') >> >> Selection: 1 >> username:*** >> password:*** >> Error in mysqlNewConnection(dbDriver(drv), ...) : >> Argument client.flag must be an integer value >> > > > -- > Joseph Fass > Bioinformatics Programmer > UC Davis Bioinformatics Core > joseph.fass -at- gmail.com (professional) > 970.227.5928 (c) || 530.752.2698 (w) >
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Hi Heidi - it seems that whenever I try to specify 3306 in the "databases.txt" file, I get this error message: > xmapConnect() Select a database to connect to: 1: Human ('homo_sapiens_core_50_36l') Selection: 1 Error in mysqlNewConnection(dbDriver(drv), ...) : Argument port must be an integer value ... this occurs whether I put double quotes around 3306 or not (all other values - not headings - in "databases.txt" have double quotes around them). Did Crispin's message mean that he fixed this particular issue? Why might I be having this issue, whereas I'm assuming other people have been using 2.0.01 successfully? ~Joe PS - I'm not very familiar with R's internals, but I went looking for the xmapConnect function, because I could run the particular line: con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = a[5], port = port, client.flag = "196608") ... if I changed it to: con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = a[5], port = port, client.flag = 196608) but apparently function code isn't stored in plain text ... UPDATE: with the help of someone more competent, we removed the quotes from 196608 in the package before re-installing, which fixed my issue ... I'm guessing this is what Crispin changed? On Mon, Dec 8, 2008 at 11:31 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote: > Hi Joseph, > > quick question; do you get the same error message when you specify which > port to use in your databases.txt file? In your first email you used 3306, > does that still apply? > > \Heidi > > > Just wanted to add that I noticed I had exonmap 2.0.0, ... so I installed > > 2.0.01, and am seeing the same error: > > > > > >> > xmapConnect() > >> Select a database to connect to: > >> > >> 1: Human ('homo_sapiens_core_50_36l') > >> > >> Selection: 1 > >> username:*** > >> password:*** > >> Error in mysqlNewConnection(dbDriver(drv), ...) : > >> Argument client.flag must be an integer value > >> > > > > > > -- > > Joseph Fass > > Bioinformatics Programmer > > UC Davis Bioinformatics Core > > joseph.fass -at- gmail.com (professional) > > 970.227.5928 (c) || 530.752.2698 (w) > > > > > -- Joseph Fass Bioinformatics Programmer UC Davis Bioinformatics Core joseph.fass -at- gmail.com (professional) 970.227.5928 (c) || 530.752.2698 (w) [[alternative HTML version deleted]]
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Hi Joseph, not sure what your issue is. Can you connect using Crispin's latest version? Both v2.0.0 and 2.0.01 works for me; I have my port as "4094" Can you please provide us with the output of sessionInfo()? \Heidi On 9 Dec 2008, at 17:10, Joseph Fass wrote: > Hi Heidi - it seems that whenever I try to specify 3306 in the > "databases.txt" file, I get this error message: > > > xmapConnect() > Select a database to connect to: > > 1: Human ('homo_sapiens_core_50_36l') > > Selection: 1 > Error in mysqlNewConnection(dbDriver(drv), ...) : > Argument port must be an integer value > > ... this occurs whether I put double quotes around 3306 or not (all > other values - not headings - in "databases.txt" have double quotes > around them). > > Did Crispin's message mean that he fixed this particular issue? > Why might I be having this issue, whereas I'm assuming other people > have been using 2.0.01 successfully? > > ~Joe > > PS - I'm not very familiar with R's internals, but I went looking > for the xmapConnect function, because I could run the particular line: > con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], > host = a[5], port = port, client.flag = "196608") > ... if I changed it to: > con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], > host = a[5], port = port, client.flag = 196608) > but apparently function code isn't stored in plain text ... > > UPDATE: with the help of someone more competent, we removed the > quotes from 196608 in the package before re-installing, which fixed > my issue ... I'm guessing this is what Crispin changed? > > > > > > > > > On Mon, Dec 8, 2008 at 11:31 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote: > Hi Joseph, > > quick question; do you get the same error message when you specify > which > port to use in your databases.txt file? In your first email you > used 3306, > does that still apply? > > \Heidi > > > Just wanted to add that I noticed I had exonmap 2.0.0, ... so I > installed > > 2.0.01, and am seeing the same error: > > > > > >> > xmapConnect() > >> Select a database to connect to: > >> > >> 1: Human ('homo_sapiens_core_50_36l') > >> > >> Selection: 1 > >> username:*** > >> password:*** > >> Error in mysqlNewConnection(dbDriver(drv), ...) : > >> Argument client.flag must be an integer value > >> > > > > > > -- > > Joseph Fass > > Bioinformatics Programmer > > UC Davis Bioinformatics Core > > joseph.fass -at- gmail.com (professional) > > 970.227.5928 (c) || 530.752.2698 (w) > > > > > > > > -- > Joseph Fass > Bioinformatics Programmer > UC Davis Bioinformatics Core > joseph.fass -at- gmail.com (professional) > 970.227.5928 (c) || 530.752.2698 (w) [[alternative HTML version deleted]]
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Hi Heidi, Thanks again for your responsiveness. I haven't tried v2.0.02; instead I had some help, and changed those lines in the xmapConnect code (see below) before installing 2.0.01 again, and I no longer have a problem (I can connect to my local copy of the database, and do analysis, etc.). The port was not a problem if I left its field in "databases.txt" as "" ... (and 3306 is the correct default for me) ... maybe this was only not a problem because there was a correct default to rely on, but in the case of client.flag, it was hardcoded into the function, and not interpreting the double quotes correctly (??) Did you mean a more recent sessionInfo? Did you get the sessionInfo and traceback results I replied with previously? sessionInfo now says: > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] exonmap_2.0.01 RMySQL_0.7-2 DBI_0.2-4 RColorBrewer_1.0-2 [5] genefilter_1.22.0 survival_2.34-1 affy_1.20.0 Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2 [4] preprocessCore_1.4.0 RSQLite_0.7-1 ~Joe On Tue, Dec 9, 2008 at 10:11 AM, Heidi Dvinge <heidi@ebi.ac.uk> wrote: > Hi Joseph, > not sure what your issue is. Can you connect using Crispin's latest > version? Both v2.0.0 and 2.0.01 works for me; I have my port as "4094" > > Can you please provide us with the output of sessionInfo()? > > \Heidi > > On 9 Dec 2008, at 17:10, Joseph Fass wrote: > > Hi Heidi - it seems that whenever I try to specify 3306 in the > "databases.txt" file, I get this error message: > > > xmapConnect() > Select a database to connect to: > > 1: Human ('homo_sapiens_core_50_36l') > > Selection: 1 > Error in mysqlNewConnection(dbDriver(drv), ...) : > Argument port must be an integer value > > ... this occurs whether I put double quotes around 3306 or not (all other > values - not headings - in "databases.txt" have double quotes around them). > > Did Crispin's message mean that he fixed this particular issue? Why might > I be having this issue, whereas I'm assuming other people have been using > 2.0.01 successfully? > > ~Joe > > PS - I'm not very familiar with R's internals, but I went looking for the > xmapConnect function, because I could run the particular line: > con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = > a[5], port = port, client.flag = "196608") > ... if I changed it to: > con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = > a[5], port = port, client.flag = 196608) > but apparently function code isn't stored in plain text ... > > UPDATE: with the help of someone more competent, we removed the quotes from > 196608 in the package before re-installing, which fixed my issue ... I'm > guessing this is what Crispin changed? > > > > > > > > > On Mon, Dec 8, 2008 at 11:31 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote: > >> Hi Joseph, >> >> quick question; do you get the same error message when you specify which >> port to use in your databases.txt file? In your first email you used 3306, >> does that still apply? >> >> \Heidi >> >> > Just wanted to add that I noticed I had exonmap 2.0.0, ... so I >> installed >> > 2.0.01, and am seeing the same error: >> > >> > >> >> > xmapConnect() >> >> Select a database to connect to: >> >> >> >> 1: Human ('homo_sapiens_core_50_36l') >> >> >> >> Selection: 1 >> >> username:*** >> >> password:*** >> >> Error in mysqlNewConnection(dbDriver(drv), ...) : >> >> Argument client.flag must be an integer value >> >> >> > >> > >> > -- >> > Joseph Fass >> > Bioinformatics Programmer >> > UC Davis Bioinformatics Core >> > joseph.fass -at- gmail.com (professional) >> > 970.227.5928 (c) || 530.752.2698 (w) >> > >> >> >> > > > -- > Joseph Fass > Bioinformatics Programmer > UC Davis Bioinformatics Core > joseph.fass -at- gmail.com (professional) > 970.227.5928 (c) || 530.752.2698 (w) > > > -- Joseph Fass Bioinformatics Programmer UC Davis Bioinformatics Core joseph.fass -at- gmail.com (professional) 970.227.5928 (c) || 530.752.2698 (w) [[alternative HTML version deleted]]
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Hi, I've just updated exonmap to version (2.0.03; 2.1.03 devel), which should fix this. Thanks for pointing it out... Crispin On 09/12/2008 18:41, "Joseph Fass" <joseph.fass at="" gmail.com=""> wrote: > Hi Heidi, > > Thanks again for your responsiveness. I haven't tried v2.0.02; instead I > had some help, and changed those lines in the xmapConnect code (see below) > before installing 2.0.01 again, and I no longer have a problem (I can > connect to my local copy of the database, and do analysis, etc.). The port > was not a problem if I left its field in "databases.txt" as "" ... (and 3306 > is the correct default for me) ... maybe this was only not a problem because > there was a correct default to rely on, but in the case of client.flag, it > was hardcoded into the function, and not interpreting the double quotes > correctly (??) > > Did you mean a more recent sessionInfo? Did you get the sessionInfo and > traceback results I replied with previously? sessionInfo now says: > >> sessionInfo() > R version 2.8.0 (2008-10-20) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;L > C_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C; LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] exonmap_2.0.01 RMySQL_0.7-2 DBI_0.2-4 > RColorBrewer_1.0-2 > [5] genefilter_1.22.0 survival_2.34-1 affy_1.20.0 > Biobase_2.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2 > [4] preprocessCore_1.4.0 RSQLite_0.7-1 > > ~Joe > > > > > > > > On Tue, Dec 9, 2008 at 10:11 AM, Heidi Dvinge <heidi at="" ebi.ac.uk=""> wrote: > >> Hi Joseph, >> not sure what your issue is. Can you connect using Crispin's latest >> version? Both v2.0.0 and 2.0.01 works for me; I have my port as "4094" >> >> Can you please provide us with the output of sessionInfo()? >> >> \Heidi >> >> On 9 Dec 2008, at 17:10, Joseph Fass wrote: >> >> Hi Heidi - it seems that whenever I try to specify 3306 in the >> "databases.txt" file, I get this error message: >> >>> xmapConnect() >> Select a database to connect to: >> >> 1: Human ('homo_sapiens_core_50_36l') >> >> Selection: 1 >> Error in mysqlNewConnection(dbDriver(drv), ...) : >> Argument port must be an integer value >> >> ... this occurs whether I put double quotes around 3306 or not (all other >> values - not headings - in "databases.txt" have double quotes around them). >> >> Did Crispin's message mean that he fixed this particular issue? Why might >> I be having this issue, whereas I'm assuming other people have been using >> 2.0.01 successfully? >> >> ~Joe >> >> PS - I'm not very familiar with R's internals, but I went looking for the >> xmapConnect function, because I could run the particular line: >> con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = >> a[5], port = port, client.flag = "196608") >> ... if I changed it to: >> con <- dbConnect("MySQL", user = un, password = pw, dbname = a[3], host = >> a[5], port = port, client.flag = 196608) >> but apparently function code isn't stored in plain text ... >> >> UPDATE: with the help of someone more competent, we removed the quotes from >> 196608 in the package before re-installing, which fixed my issue ... I'm >> guessing this is what Crispin changed? >> >> >> >> >> >> >> >> >> On Mon, Dec 8, 2008 at 11:31 PM, Heidi Dvinge <heidi at="" ebi.ac.uk=""> wrote: >> >>> Hi Joseph, >>> >>> quick question; do you get the same error message when you specify which >>> port to use in your databases.txt file? In your first email you used 3306, >>> does that still apply? >>> >>> \Heidi >>> >>>> Just wanted to add that I noticed I had exonmap 2.0.0, ... so I >>> installed >>>> 2.0.01, and am seeing the same error: >>>> >>>> >>>>>> xmapConnect() >>>>> Select a database to connect to: >>>>> >>>>> 1: Human ('homo_sapiens_core_50_36l') >>>>> >>>>> Selection: 1 >>>>> username:*** >>>>> password:*** >>>>> Error in mysqlNewConnection(dbDriver(drv), ...) : >>>>> Argument client.flag must be an integer value >>>>> >>>> >>>> >>>> -- >>>> Joseph Fass >>>> Bioinformatics Programmer >>>> UC Davis Bioinformatics Core >>>> joseph.fass -at- gmail.com (professional) >>>> 970.227.5928 (c) || 530.752.2698 (w) >>>> >>> >>> >>> >> >> >> -- >> Joseph Fass >> Bioinformatics Programmer >> UC Davis Bioinformatics Core >> joseph.fass -at- gmail.com (professional) >> 970.227.5928 (c) || 530.752.2698 (w) >> >> >> > -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}
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Hi, I've just fixed this - in version 2.0.02 (or for the devl version - 2.1.02) - it should appear in the repository soon... cheers, Crispin On 09/12/2008 07:31, "Heidi Dvinge" <heidi at="" ebi.ac.uk=""> wrote: > Hi Joseph, > > quick question; do you get the same error message when you specify which > port to use in your databases.txt file? In your first email you used 3306, > does that still apply? > > \Heidi > >> Just wanted to add that I noticed I had exonmap 2.0.0, ... so I installed >> 2.0.01, and am seeing the same error: >> >> >>>> xmapConnect() >>> Select a database to connect to: >>> >>> 1: Human ('homo_sapiens_core_50_36l') >>> >>> Selection: 1 >>> username:*** >>> password:*** >>> Error in mysqlNewConnection(dbDriver(drv), ...) : >>> Argument client.flag must be an integer value >>> >> >> >> -- >> Joseph Fass >> Bioinformatics Programmer >> UC Davis Bioinformatics Core >> joseph.fass -at- gmail.com (professional) >> 970.227.5928 (c) || 530.752.2698 (w) >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}
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