Entering edit mode
Hi everyone,
I have problem in reproducing vignette example from MeSHDbi package.
That is, when I run:
> example("makeGeneMeSHPackage")
It should use preformatted data frames "PAO1" and "metaPAO1" to construct custom org.MeSH.XXX.db package that can subsequently be loaded via library() and queried with Annotation.dbi or RSQLite, or at least that is how other org.MeSH.XXX.db packages behave (org.MeSH.Hsa.db, for instance).
but
> example("makeGeneMeSHPackage")
mGMSHP> ## makeGeneMeSHPackage enable users to construct
mGMSHP> ## user's own custom MeSH package
mGMSHP>
mGMSHP> ## this is test data which means the relationship between
mGMSHP> ## Entrez gene IDs of Pseudomonas aeruginosa PAO1
mGMSHP> ## and its MeSH IDs.
mGMSHP> data(PAO1)
mGMSHP> head(PAO1)
GENEID MESHID MESHCATEGORY SOURCEID
1 877657 D000265 D 937805
2 877657 D000265 D 937805
3 877657 D001412 B 937805
4 877657 D001412 B 937805
5 877657 D001426 D 937805
6 877657 D001483 G 937805
SOURCEDB
1 Bacillus subtilis subsp. spizizenii str. 168
2 Bacillus subtilis subsp. spizizenii str. 168
3 Bacillus subtilis subsp. spizizenii str. 168
4 Bacillus subtilis subsp. spizizenii str. 168
5 Bacillus subtilis subsp. spizizenii str. 168
6 Bacillus subtilis subsp. spizizenii str. 168
mGMSHP> # We are also needed to prepare meta data as follows.
mGMSHP> data(metaPAO1)
mGMSHP> metaPAO1
NAME
1 SOURCEDATE
2 SOURCENAME
3 SOURCEURL
4 DBSCHEMA
5 DBSCHEMAVERSION
6 ORGANISM
7 SPECIES
8 package
9 Db type
VALUE
1 31-July-2013
2 BLASTP
3 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
4 org.Pae.PAO1.MeSH.db
5 1.0
6 Pseudomonas aeruginosa PAO1
7
8 AnnotationDbi
9 BLASTDb
mGMSHP> ## sets up a temporary directory for this example
mGMSHP> ## (users won't need to do this step)
mGMSHP> destination <- tempfile()
mGMSHP> dir.create(destination)
mGMSHP> ## makes an Organism package for human called Homo.sapiens
mGMSHP> makeGeneMeSHPackage(pkgname = "org.MeSH.Pae.db",
mGMSHP+ data = PAO1,
mGMSHP+ metadata = metaPAO1,
mGMSHP+ organism = "Pseudomonas aeruginosa PAO1",
mGMSHP+ version = "1.0.0",
mGMSHP+ maintainer = "Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>",
mGMSHP+ author = "Koki Tsuyuzaki",
mGMSHP+ destDir = destination,
mGMSHP+ license="Artistic-2.0")
Creating package in /var/folders/19/6n33ytjd6nd1m9rtrt6plcfm0000gn/T//RtmpFLPUeT/filef4160c94d3/org.MeSH.Pae.db
[1] TRUE
Warning messages:
1: 'dbBeginTransaction' is deprecated.
Use 'dbBegin' instead.
See help("Deprecated")
2: 'dbBeginTransaction' is deprecated.
Use 'dbBegin' instead.
See help("Deprecated")
so when I try to load it, it says:
> library("org.MeSH.Pae.db")
Error in library("org.MeSH.Pae.db") :
‘org.MeSH.Pae.db’ is not a valid installed package
could someone give me a clue what went wrong? Should there be another sequence of commands that should "install" this package properly?
I would really appreciate any help with this.
Best,
Svetlana Bojic, MD
session info output is below:
> sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) 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] grid parallel stats graphics [5] grDevices utils datasets methods [9] base other attached packages: [1] meshr_1.0.4 [2] org.MeSH.Syn.db_1.0.0 [3] org.MeSH.Bsu.168.db_1.0.0 [4] org.MeSH.Atu.K84.db_1.0.0 [5] org.MeSH.Aca.db_1.0.0 [6] org.MeSH.Hsa.db_1.0.0 [7] org.Hs.eg.db_2.14.0 [8] cummeRbund_2.6.1 [9] Gviz_1.8.4 [10] rtracklayer_1.24.2 [11] GenomicRanges_1.16.4 [12] IRanges_1.22.10 [13] fastcluster_1.1.16 [14] reshape2_1.4.1 [15] ggplot2_1.0.0 [16] Category_2.30.0 [17] GO.db_2.14.0 [18] RSQLite_1.0.0 [19] Matrix_1.1-5 [20] fdrtool_1.2.13 [21] MeSH.PCR.db_1.0.0 [22] MeSH.db_1.0.1 [23] MeSH.AOR.db_1.0.0 [24] MeSHDbi_1.0.2 [25] GSEABase_1.26.0 [26] graph_1.42.0 [27] annotate_1.42.1 [28] AnnotationDbi_1.26.1 [29] GenomeInfoDb_1.0.2 [30] Biobase_2.24.0 [31] BiocGenerics_0.10.0 [32] limma_3.20.9 [33] phyloseq_1.8.2 [34] RMySQL_0.10.2 [35] DBI_0.3.1 [36] viz14_0.0.10 loaded via a namespace (and not attached): [1] acepack_1.3-3.3 [2] ade4_1.6-2 [3] ape_3.2 [4] assertthat_0.1 [5] base64enc_0.1-2 [6] BatchJobs_1.5 [7] BBmisc_1.9 [8] BiocParallel_0.6.1 [9] biom_0.3.12 [10] biomaRt_2.20.0 [11] Biostrings_2.32.1 [12] biovizBase_1.12.3 [13] bitops_1.0-6 [14] brew_1.0-6 [15] BSgenome_1.32.0 [16] checkmate_1.5.1 [17] cluster_2.0.1 [18] codetools_0.2-10 [19] colorspace_1.2-5 [20] data.table_1.9.2 [21] DESeq2_1.4.5 [22] dichromat_2.0-0 [23] digest_0.6.8 [24] dplyr_0.4.1 [25] fail_1.2 [26] foreach_1.4.2 [27] foreign_0.8-63 [28] Formula_1.2-0 [29] genefilter_1.46.1 [30] geneplotter_1.42.0 [31] GenomicAlignments_1.0.6 [32] GenomicFeatures_1.16.3 [33] GenomicFiles_1.0.1 [34] ggbio_1.12.10 [35] ggvis_0.4 [36] gridExtra_0.9.1 [37] gtable_0.1.2 [38] Heatplus_2.10.0 [39] Hmisc_3.15-0 [40] htmltools_0.2.6 [41] httpuv_1.3.2 [42] igraph_0.7.1 [43] iterators_1.0.7 [44] lattice_0.20-30 [45] latticeExtra_0.6-26 [46] locfit_1.5-9.1 [47] magrittr_1.5 [48] MASS_7.3-39 [49] matrixStats_0.14.0 [50] mgcv_1.8-5 [51] mime_0.2 [52] multtest_2.20.0 [53] munsell_0.4.2 [54] nlme_3.1-120 [55] nnet_7.3-9 [56] parody_1.22.0 [57] permute_0.8-3 [58] plyr_1.8.1 [59] proto_0.3-10 [60] R6_2.0.1 [61] RBGL_1.40.1 [62] RColorBrewer_1.1-2 [63] Rcpp_0.11.4 [64] RcppArmadillo_0.4.650.1.1 [65] RCurl_1.95-4.5 [66] RJSONIO_1.3-0 [67] rpart_4.1-9 [68] Rsamtools_1.16.1 [69] scales_0.2.4 [70] sendmailR_1.2-1 [71] shiny_0.11.1 [72] SparseM_1.6 [73] splines_3.1.0 [74] stats4_3.1.0 [75] stringr_0.6.2 [76] survival_2.38-1 [77] tcltk_3.1.0 [78] tools_3.1.0 [79] topGO_2.16.0 [80] VariantAnnotation_1.10.5 [81] vegan_2.2-1 [82] XML_3.98-1.1 [83] xtable_1.7-4 [84] XVector_0.4.0 [85] zlibbioc_1.10.0
