Dear Marc and Hervé,
I believe the AnnotationForge package is currently not working correctly. Perhaps due to an update in SQL functions? To keep it as simple as possible, I simply tried to reproduce the worked example in Marc's "Making Organism packages" vignette. It required one small modification on the last line to run (type="source"), so I'll paste in the whole code here:
library(AnnotationForge) ## Makes an organism package for Zebra Finch data.frames: finchFile <- system.file("extdata","finch_info.txt", package="AnnotationForge") finch <- read.table(finchFile,sep="\t") ## Now prepare some data.frames fSym <- finch[,c(2,3,9)] fSym <- fSym[fSym[,2]!="-",] fSym <- fSym[fSym[,3]!="-",] colnames(fSym) <- c("GID","SYMBOL","GENENAME") fChr <- finch[,c(2,7)] fChr <- fChr[fChr[,2]!="-",] colnames(fChr) <- c("GID","CHROMOSOME") finchGOFile <- system.file("extdata","GO_finch.txt", package="AnnotationForge") fGO <- read.table(finchGOFile,sep="\t") fGO <- fGO[fGO[,2]!="",] fGO <- fGO[fGO[,3]!="",] colnames(fGO) <- c("GID","GO","EVIDENCE") ## Then call the function makeOrgPackage(gene_info=fSym, chromosome=fChr, go=fGO, version="0.1", maintainer="Some One <firstname.lastname@example.org>", author="Some One <email@example.com>", outputDir = ".", tax_id="59729", genus="Taeniopygia", species="guttata", goTable="go") ## then you can call install.packages based on the return value install.packages("./org.Tguttata.eg.db", repos=NULL, type="source")
No errors, but 50+ warnings like this:
In result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
I can load the resulting package, but the database seems to be empty:
Quality control information for org.Tguttata.eg: This package has the following mappings: Additional Information about this package: DB schema: NOSCHEMA_DB DB schema version: 2.1 Organism: Taeniopygia guttata
At the end of this message, I'm posting my sessionInfo().
Many thanks for all the great work, and I hope this post helps getting others unstuck as well.
PS Thinking the RSQLite package might have been updated and become incompatible, I also tried running the same code on an old R (3.4) installation on Linux, but got similar warnings although mentioning different SQL functions, and the result was equally unpopulated.
R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.4 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  org.Tguttata.eg.db_0.1 AnnotationForge_1.28.0 AnnotationDbi_1.48.0 IRanges_2.20.2 S4Vectors_0.24.4  Biobase_2.46.0 BiocGenerics_0.32.0 loaded via a namespace (and not attached):  Rcpp_1.0.4 GO.db_3.10.0 XML_3.99-0.3 digest_0.6.25 bitops_1.0-6 DBI_1.1.0 RSQLite_2.2.0  rlang_0.4.5 blob_1.2.1 vctrs_0.2.4 tools_3.6.2 bit64_0.9-7 RCurl_1.98-1.2 bit_1.1-15.2  compiler_3.6.2 pkgconfig_2.0.3 memoise_1.1.0