Hi Marc, And thanks for helping me out. Since you told me you had no problem producing the annotation package with my IDs I also run the package with another computer and had no problem with that. When I compared the folder structures of the problematic package and the correct one I realized that the problematic package contained a folder named "r" while the correct one had a folder called "R". I got a new laptop very recently and it's running both Windows and Linux. Most of the hard disk (where I keep all my data) is configured to be readable by both systems. As it appears, in this file system (vfat) folder names with only capital letters aren't accepted and are automatically changed into lower-case. I can of course get around the problem by choosing another location for the produced annotation package. It just turned out to be difficult for me to spot this problem and it took me some time (more than it probably should have taken!). So thanks again, Asta ----- Original Message ----- From: Marc Carlson <mcarlson@fhcrc.org> Date: Saturday, February 7, 2009 0:25 am Subject: Re: [BioC] Problem using SQLForge for creating a custom annotation package To: Asta Laiho <astlai at="" utu.fi=""> Cc: bioconductor at stat.math.ethz.ch > 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=e n_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_ID ENTIFICATION=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 > > > > _______________________________________________ > > 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 > > > > >