[BioC] Problem using SQLForge for creating a custom annotation package
Marc Carlson
mcarlson at fhcrc.org
Fri Feb 6 23:24:45 CET 2009
Hi Asta,
I took your 5 lines of IDs, and made a tab delimited file. Then ran
your code and produced a very small package that I installed. But my
package seems to have retained its R directory and seems to work just fine.
>From your description the trouble seems to have happened after you
installed it.
After you made the package you must have ran 'R CMD INSTALL
testpackage.db/' to install it. Could you please share with me the
output from that command?
Also, could you please run 'R CMD check testpackage.db/' for me and
share the output from that?
One other difference between us (that I would guess does not matter) is
that my version of Biobase is slightly newer than yours (Biobase_2.2.2) .
Marc
Asta Laiho wrote:
> Dear all,
>
> I have been trying to use SQLForge package for creating a custom annotation package. No error messages can be seen when the package is created and I'm also able to install it without errors. But when I try to load the library it gives me the following errors:
>
> # library(testpackage.db)
> # Error in namespaceExport(ns, exports) :
> # undefined exports: testpackage, testpackage_dbconn, testpackage_dbfile, testpackage_dbschema, testpackage_dbInfo, testpackageORGANISM
> # In addition: Warning message:
> # In loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) :
> # package 'testpackage.db' contains no R code
> # Error: package/namespace load failed for 'testpackage.db'
>
> When I look at the folder structure under \usr\lib\R\library\testpackage, the R folder indeed seems to be missing:
>
> |-- CONTENTS
> |-- DESCRIPTION
> |-- INDEX
> |-- Meta
> |-- NAMESPACE
> |-- R-ex
> |-- extdata
> |-- help
> |-- html
> |-- latex
> `-- man
>
> I would be very delighted if someone would be able to tell me what causes the problem or where I go wrong. More detailed information can be found below if needed.
>
> - Asta
>
> -------------------------------------------------------------------
>
> This is how creating the annotation package looks:
>
> # > makeHUMANCHIP_DB(
> # + affy=FALSE,
> # + prefix="testpackage",
> # + fileName="./temp/mapFile",
> # + baseMapType="gbNRef",
> # + outputDir=".",
> # + version="1.0.0",
> # + chipName="test",
> # + )
> # baseMapType is gb or gbNRef
> # Prepending Metadata
> # Creating Genes table
> # Appending Probes
> # Found 28459 Probe Accessions
> # Appending Gene Info
> # Found 27958 Gene Names
> # Found 27958 Gene Symbols
> # Appending Chromosomes
> # Appending Cytogenetic Locations
> # Appending Omim
> # Appending RefSeq
> # Appending Pubmed
> # Appending Unigene
> # Appending ChrLengths
> # Appending 3 GO tables
> # Appending 3 GO ALL tables
> # Appending KEGG
> # Appending EC
> # Appending Chromosome Locations
> # Appending Pfam
> # Appending Prosite
> # Appending Alias
> # Appending Ensembl
> # Appending Uniprot
> # Appending Metadata
> #
> #
> # Creating package in ./testpackage.db
>
> ------------------------------------------------------
>
> The id source file looks like this (five first rows):
>
> V1 V2
> 1 chr1:000757897-000757941 BC086872
> 2 SAMD11 NM_152486
> 3 NOC2L NM_015658
> 4 PLEKHN1 NM_032129
> 5 HES4-ISG15 NM_021170
>
> ------------------------------------------------------
>
> The folder content before installing with R CMD INSTALL looks like the following:
>
> testpackage.db/
> |-- DESCRIPTION
> |-- NAMESPACE
> |-- inst
> | `-- extdata
> | `-- testpackage.sqlite
> |-- man
> | |-- testpackageACCNUM.Rd
> | |-- testpackageALIAS2PROBE.Rd
> | |-- testpackageBASE.Rd
> | |-- testpackageCHR.Rd
> | |-- testpackageCHRLENGTHS.Rd
> | |-- testpackageCHRLOC.Rd
> | |-- testpackageENSEMBL.Rd
> | |-- testpackageENTREZID.Rd
> | |-- testpackageENZYME.Rd
> | |-- testpackageENZYME2PROBE.Rd
> | |-- testpackageGENENAME.Rd
> | |-- testpackageGO.Rd
> | |-- testpackageGO2ALLPROBES.Rd
> | |-- testpackageGO2PROBE.Rd
> | |-- testpackageMAP.Rd
> | |-- testpackageMAPCOUNTS.Rd
> | |-- testpackageOMIM.Rd
> | |-- testpackageORGANISM.Rd
> | |-- testpackagePATH.Rd
> | |-- testpackagePATH2PROBE.Rd
> | |-- testpackagePFAM.Rd
> | |-- testpackagePMID.Rd
> | |-- testpackagePMID2PROBE.Rd
> | |-- testpackagePROSITE.Rd
> | |-- testpackageREFSEQ.Rd
> | |-- testpackageSYMBOL.Rd
> | |-- testpackageUNIGENE.Rd
> | |-- testpackageUNIPROT.Rd
> | `-- testpackage_dbconn.Rd
> `-- r
> `-- zzz.R
>
> -------------------------------------------------------------------
>
> after installing the package the full folder structure under \usr\lib\R\library\testpackage:
>
> usr/lib/R/library/testpackage.db/
> |-- CONTENTS
> |-- DESCRIPTION
> |-- INDEX
> |-- Meta
> | |-- Rd.rds
> | |-- hsearch.rds
> | |-- nsInfo.rds
> | `-- package.rds
> |-- NAMESPACE
> |-- R-ex
> | |-- testpackageACCNUM.R
> | |-- testpackageALIAS2PROBE.R
> | |-- testpackageBASE.R
> | |-- testpackageCHR.R
> | |-- testpackageCHRLENGTHS.R
> | |-- testpackageCHRLOC.R
> | |-- testpackageENSEMBL.R
> | |-- testpackageENTREZID.R
> | |-- testpackageENZYME.R
> | |-- testpackageENZYME2PROBE.R
> | |-- testpackageGENENAME.R
> | |-- testpackageGO.R
> | |-- testpackageGO2ALLPROBES.R
> | |-- testpackageGO2PROBE.R
> | |-- testpackageMAP.R
> | |-- testpackageMAPCOUNTS.R
> | |-- testpackageOMIM.R
> | |-- testpackageORGANISM.R
> | |-- testpackagePATH.R
> | |-- testpackagePATH2PROBE.R
> | |-- testpackagePFAM.R
> | |-- testpackagePMID.R
> | |-- testpackagePMID2PROBE.R
> | |-- testpackagePROSITE.R
> | |-- testpackageREFSEQ.R
> | |-- testpackageSYMBOL.R
> | |-- testpackageUNIGENE.R
> | |-- testpackageUNIPROT.R
> | `-- testpackage_dbconn.R
> |-- extdata
> | `-- testpackage.sqlite
> |-- help
> | |-- AnIndex
> | |-- testpackageACCNUM
> | |-- testpackageALIAS2PROBE
> | |-- testpackageBASE
> | |-- testpackageCHR
> | |-- testpackageCHRLENGTHS
> | |-- testpackageCHRLOC
> | |-- testpackageENSEMBL
> | |-- testpackageENTREZID
> | |-- testpackageENZYME
> | |-- testpackageENZYME2PROBE
> | |-- testpackageGENENAME
> | |-- testpackageGO
> | |-- testpackageGO2ALLPROBES
> | |-- testpackageGO2PROBE
> | |-- testpackageMAP
> | |-- testpackageMAPCOUNTS
> | |-- testpackageOMIM
> | |-- testpackageORGANISM
> | |-- testpackagePATH
> | |-- testpackagePATH2PROBE
> | |-- testpackagePFAM
> | |-- testpackagePMID
> | |-- testpackagePMID2PROBE
> | |-- testpackagePROSITE
> | |-- testpackageREFSEQ
> | |-- testpackageSYMBOL
> | |-- testpackageUNIGENE
> | |-- testpackageUNIPROT
> | `-- testpackage_dbconn
> |-- html
> | |-- 00Index.html
> | |-- testpackageACCNUM.html
> | |-- testpackageALIAS2PROBE.html
> | |-- testpackageBASE.html
> | |-- testpackageCHR.html
> | |-- testpackageCHRLENGTHS.html
> | |-- testpackageCHRLOC.html
> | |-- testpackageENSEMBL.html
> | |-- testpackageENTREZID.html
> | |-- testpackageENZYME.html
> | |-- testpackageENZYME2PROBE.html
> | |-- testpackageGENENAME.html
> | |-- testpackageGO.html
> | |-- testpackageGO2ALLPROBES.html
> | |-- testpackageGO2PROBE.html
> | |-- testpackageMAP.html
> | |-- testpackageMAPCOUNTS.html
> | |-- testpackageOMIM.html
> | |-- testpackageORGANISM.html
> | |-- testpackagePATH.html
> | |-- testpackagePATH2PROBE.html
> | |-- testpackagePFAM.html
> | |-- testpackagePMID.html
> | |-- testpackagePMID2PROBE.html
> | |-- testpackagePROSITE.html
> | |-- testpackageREFSEQ.html
> | |-- testpackageSYMBOL.html
> | |-- testpackageUNIGENE.html
> | |-- testpackageUNIPROT.html
> | `-- testpackage_dbconn.html
> |-- latex
> | |-- testpackageACCNUM.tex
> | |-- testpackageALIAS2PROBE.tex
> | |-- testpackageBASE.tex
> | |-- testpackageCHR.tex
> | |-- testpackageCHRLENGTHS.tex
> | |-- testpackageCHRLOC.tex
> | |-- testpackageENSEMBL.tex
> | |-- testpackageENTREZID.tex
> | |-- testpackageENZYME.tex
> | |-- testpackageENZYME2PROBE.tex
> | |-- testpackageGENENAME.tex
> | |-- testpackageGO.tex
> | |-- testpackageGO2ALLPROBES.tex
> | |-- testpackageGO2PROBE.tex
> | |-- testpackageMAP.tex
> | |-- testpackageMAPCOUNTS.tex
> | |-- testpackageOMIM.tex
> | |-- testpackageORGANISM.tex
> | |-- testpackagePATH.tex
> | |-- testpackagePATH2PROBE.tex
> | |-- testpackagePFAM.tex
> | |-- testpackagePMID.tex
> | |-- testpackagePMID2PROBE.tex
> | |-- testpackagePROSITE.tex
> | |-- testpackageREFSEQ.tex
> | |-- testpackageSYMBOL.tex
> | |-- testpackageUNIGENE.tex
> | |-- testpackageUNIPROT.tex
> | `-- testpackage_dbconn.tex
> `-- man
> `-- testpackage.db.Rd.gz
>
>
> ------------------------------------------------------
>
> and finally my session info:
>
> R version 2.8.1 (2008-12-22)
> i386-redhat-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_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.2
> [4] Biobase_2.2.1
>
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