[BioC] Problem using SQLForge for creating a custom annotation package
Asta Laiho
astlai at utu.fi
Fri Feb 6 15:47:14 CET 2009
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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