[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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