It appears that your org.Hs.eg.db and GO.db packages are still v3.4.2. Please run the command BiocInstaller::biocLite() to update your packages to the new version (v3.5.0).
________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Yu, Guangchuang <g...@connect.hku.hk> Sent: Thursday, November 2, 2017 8:40:31 AM To: bioc-devel Subject: [Bioc-devel] annotation data not updated? Dear all, I just upgraded BioC to 3.6 and found that the data source of org.Hs.eg.db and GO.db is still half year ago. I was wondering whether these packages had been updated in current release. > org.Hs.eg.db OrgDb object: | DBSCHEMAVERSION: 2.1 | Db type: OrgDb | Supporting package: AnnotationDbi | DBSCHEMA: HUMAN_DB | ORGANISM: Homo sapiens | SPECIES: Human | EGSOURCEDATE: *2017-Mar29* | EGSOURCENAME: Entrez Gene | EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA | CENTRALID: EG | TAXID: 9606 | GOSOURCENAME: Gene Ontology | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ | GOSOURCEDATE: *2017-Mar29* | GOEGSOURCEDATE: 2017-Mar29 | GOEGSOURCENAME: Entrez Gene | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA | KEGGSOURCENAME: KEGG GENOME | KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes | KEGGSOURCEDATE: 2011-Mar15 | GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens) | GPSOURCEURL: | GPSOURCEDATE: 2017-Sep7 | ENSOURCEDATE: 2017-Mar29 | ENSOURCENAME: Ensembl | ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta | UPSOURCENAME: Uniprot | UPSOURCEURL: http://www.UniProt.org/ | UPSOURCEDATE: Thu Oct 5 16:07:33 2017 Please see: help('select') for usage information > GO.db GODb object: | GOSOURCENAME: Gene Ontology | GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ | GOSOURCEDATE: *2017-Mar29* | Db type: GODb | package: AnnotationDbi | DBSCHEMA: GO_DB | GOEGSOURCEDATE: 2017-Mar29 | GOEGSOURCENAME: Entrez Gene | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA | DBSCHEMAVERSION: 2.1 Please see: help('select') for usage information > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] org.Hs.eg.db_3.4.2 GO.db_3.4.2 AnnotationDbi_1.40.0 [4] IRanges_2.12.0 S4Vectors_0.16.0 Biobase_2.38.0 [7] BiocGenerics_0.24.0 rvcheck_0.0.9 rmarkdown_1.6 [10] roxygen2_6.0.1 magrittr_1.5 BiocInstaller_1.28.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.13 knitr_1.17 xml2_1.1.1 bit_1.1-12 [5] R6_2.2.2 rlang_0.1.2 blob_1.1.0 stringr_1.2.0 [9] tools_3.4.2 DBI_0.7 htmltools_0.3.6 commonmark_1.4 [13] bit64_0.9-7 rprojroot_1.2 digest_0.6.12 tibble_1.3.4 [17] memoise_1.1.0 RSQLite_2.0 evaluate_0.10.1 stringi_1.1.5 [21] compiler_3.4.2 backports_1.1.1 pkgconfig_2.0.1 > -- --~--~---------~--~----~------------~-------~--~----~ Guangchuang Yu PhD Postdoc researcher State Key Laboratory of Emerging Infectious Diseases School of Public Health The University of Hong Kong Hong Kong SAR, China www: https://guangchuangyu.github.io -~----------~----~----~----~------~----~------~--~--- [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
