[BioC] biomart scripting help
Steffen Durinck
durincks at mail.nih.gov
Fri Nov 24 18:01:41 CET 2006
Hi Ariel,
It says:
Manually specify the location of the MySQL
libraries and the header files and re-run R CMD INSTALL.
Did you set these environment variables before trying the installation?
Best,
Steffen
Ariel Chernomoretz wrote:
>
> Hi,
>
> This is what I get from R (same things from shell prompt installation)
>
> > source("http://www.bioconductor.org/biocLite.R")
> > biocLite("RMySQL")
> Running getBioC version 0.1.8 with R version 2.4.0
> Running biocinstall version 1.9.9 with R version 2.4.0
> Your version of R requires version 1.9 of Bioconductor.
> trying URL
> 'http://cran.us.r-project.org/src/contrib/RMySQL_0.5-10.tar.gz'
> <http://cran.us.r-project.org/src/contrib/RMySQL_0.5-10.tar.gz%27>
> Content type 'application/x-tar' length 142671 bytes
> opened URL
> ==================================================
> downloaded 139Kb
>
> * Installing *source* package 'RMySQL' ...
> creating cache ./config.cache
> checking how to run the C preprocessor... cc -E
> checking for compress in -lz... yes
> checking for getopt_long in -lc... yes
> checking for mysql_init in -lmysqlclient... no
> checking for mysql.h... no
> checking for mysql_init in -lmysqlclient... no
> checking for mysql_init in -lmysqlclient... no
> checking for mysql_init in -lmysqlclient... no
> checking for mysql_init in -lmysqlclient... no
> checking for mysql_init in -lmysqlclient... no
> checking for /usr/local/include/mysql/mysql.h... no
> checking for /usr/include/mysql/mysql.h... no
> checking for /usr/local/mysql/include/mysql/mysql.h... no
> checking for /opt/include/mysql/mysql.h... no
> checking for /include/mysql/mysql.h... no
>
> Configuration error:
> could not find the MySQL installation include and/or library
> directories. Manually specify the location of the MySQL
> libraries and the header files and re-run R CMD INSTALL.
>
>
> So it seems it is looking for mysql.h, and probably other include
> files, that are missing in my system:
>
> [ariel at LAB309-10 ~]$ locate mysql.h
> /usr/share/doc/selinux-policy-2.2.23/html/services_mysql.html
>
>
> [ariel at LAB309-10 ~]$ rpm -ql mysql | grep mysql?h
> [ariel at LAB309-10 ~]$ rpm -ql mysql | grep mysql.h
> /usr/bin/mysqlcheck
> /usr/bin/mysqlshow
> /usr/share/man/man1/mysqlshow.1.gz
> /usr/share/mysql/hungarian
> /usr/share/mysql/hungarian/errmsg.sys
>
>
> best
>
> Ariel./
>
>
>
>
>
> -----Original Message-----
> From: Steffen Durinck [mailto:durincks at mail.nih.gov]
> Sent: Fri 11/24/2006 11:40 AM
> To: Ariel Chernomoretz
> Cc: marco fabbri; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] biomart scripting help
>
> Hi Ariel,
>
> You should have enough by having the MySQL client installed.
> Did the installation of RMySQL give any errors?
> Try installing the RMySQL package from command line with R CMD INSTALL.
> It should tell you which environment variables need to be set to point R
> to your MySQL client installation.
>
> Best,
> Steffen
>
> Ariel Chernomoretz wrote:
> >
> > Hi Marco, Steffen,
> >
> > I was following your thread, because I want to do the same homology
> > mapping using biomaRt.
> > However I am kind of stuck because I could not install RMySql.
> > It seems that mysql.h is missing in my system.
> >
> > I am running a Fedora Core 5 Linux , and I think I have only the
> > client stuff of mysql.
> > Should I get the server version installed? Binary or
> source-and-compiled?
> > would that interfere with the already installed mysql soft I have here?
> >
> > Any help would be appreciated.
> > Regards
> > Ariel./
> >
> >
> >
> > -----Original Message-----
> > From: bioconductor-bounces at stat.math.ethz.ch on behalf of marco fabbri
> > Sent: Fri 11/24/2006 10:21 AM
> > To: Steffen Durinck
> > Cc: bioconductor at stat.math.ethz.ch
> > Subject: Re: [BioC] biomart scripting help
> >
> > Thank you,
> > this solved my problem.
> > For the second part of my problem.
> > I try to get some annotation on the two lists
> > the starting list (in this example homolog[,1]) and the results list
> > (homolg[,2])
> >
> > I can use
> > annotation= getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol",
> > "chromosome_name",
> > "band"), filters = "affy_hg_u95av2", values = homolog[,1], mart =
> human)
> > show(annotation)
> > affy_hg_u95av2 hgnc_symbol chromosome_name band
> > 1 1939_at TP53 17 p13.1
> >
> > ... but I can not to create a single table with cbind(homolog,
> > annotation), I would like to have a NA for gene not founded and for
> > repeated ID, repeated annotation.
> >
> > thanks Marco
> >
> >
> >
> > On 24/11/06, Steffen Durinck <durincks at mail.nih.gov> wrote:
> > > Hi Marco,
> > >
> > > If you use biomaRt in MySQL mode for this query you will get both the
> > > affy_mouse430_2 and affy_hg_u95av2 ids in the result.
> > > The reason why this doesn't happen in the webservice (default) mode is
> > > that the BioMart webservice currently doesn't allow this, however I
> > > expect this to change in the near future.
> > >
> > > You'll need to install RMySQL, then try:
> > >
> > > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl",
> > mysql=TRUE)
> > > mouse=useMart("ensembl", dataset = "mmusculus_gene_ensembl",
> mysql=TRUE)
> > > homolog = getHomolog( id = c("1939_at","2000_at"), to.array
> > > ="affy_mouse430_2", from.array ="affy_hg_u95av2",from.mart = human,
> > > to.mart = mouse )
> > >
> > > You should get:
> > >
> > > > homolog
> > > id MappedID
> > > 1 1939_at 1427739_a_at
> > > 2 1939_at 1426538_a_at
> > > 3 2000_at 1428830_at
> > > 4 2000_at 1421205_at
> > >
> > >
> > > Cheers,
> > > Steffen
> > >
> > >
> > >
> > >
> > >
> > > marco fabbri wrote:
> > > > I looking for help on biomRt.
> > > > I am starting from a human affy code list and I would like to
> have the
> > > > mouse homologue.
> > > > If I am running this script I do not know which probe is
> homologue to
> > > >
> > > >
> > > >> homolog = getHomolog( id = c("1939_at","2000_at"), to.array =
> > > >>
> > > > "affy_mouse430_2 ", from.array ="affy_hg_u95av2",
> > > > from.mart = human, to.mart = mouse )
> > > >
> > > >
> > > >> show(homolog)
> > > >>
> > > > V1
> > > > 1 1427739_a_at
> > > > 2 1426538_a_at
> > > > 3 1428830_at
> > > > 4 1421205_at
> > > >
> > > > I also tried with getBM but no success..
> > > > My ideal result would be: from a humann affy id list to get a
> > table like that:
> > > >
> > > > human_probesets -- human_gene_name -- homol_mouse_probesets --
> > > > homolog_mouse_gene_name
> > > >
> > > > Thank Marco
> > > >
> > > > _______________________________________________
> > > > 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
> > > >
> > >
> > >
> >
> >
> > --
> > ---------------------------------------
> > Marco Fabbri
> > Istituto Clinico Humanitas
> > via Manzoni, 52
> > 20089 Rozzano (Mi)
> > Tel. 028224 5152
> > Fax 028224 5101
> >
> > _______________________________________________
> > 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
> >
>
>
> --
> Steffen Durinck, Ph.D.
>
> Oncogenomics Section
> Pediatric Oncology Branch
> National Cancer Institute, National Institutes of Health
> URL: http://home.ccr.cancer.gov/oncology/oncogenomics/
>
> Phone: 301-402-8103
> Address:
> Advanced Technology Center,
> 8717 Grovemont Circle
> Gaithersburg, MD 20877
>
--
Steffen Durinck, Ph.D.
Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/
Phone: 301-402-8103
Address:
Advanced Technology Center,
8717 Grovemont Circle
Gaithersburg, MD 20877
More information about the Bioconductor
mailing list