[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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