Hi,
I am trying to install the annotation mogene10sttranscriptcluster.db from the recent release as followed:
biocLite("mogene10sttranscriptcluster")
It seems to install properly because I didn't get any error message. But when I loaded the annotation package, I couldn't find any of the annotation content (ie ACCNUM, CHR, ALIAS2PROBE, GENENAME etc):
> head(ls("package:mogene10sttranscriptcluster.db"))
[1] "mogene10sttranscriptcluster" "mogene10sttranscriptcluster_dbconn"
[3] "mogene10sttranscriptcluster_dbfile" "mogene10sttranscriptcluster_dbInfo"
[5] "mogene10sttranscriptcluster_dbschema" "mogene10sttranscriptcluster.db"
I tried to reinstall from the source package, but I had the same problem. Would appreciate any suggestion.
Below is my session:
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.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] stats4 parallel stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] mogene10sttranscriptcluster.db_8.7.0 org.Mm.eg.db_3.5.0
[3] AnnotationDbi_1.40.0 ggplot2_2.2.1
[5] RColorBrewer_1.1-2 gplots_3.0.1
[7] BiocInstaller_1.28.0 pd.mta.1.0_3.12.0
[9] DBI_0.7 RSQLite_2.0
[11] oligo_1.42.0 Biostrings_2.46.0
[13] XVector_0.18.0 IRanges_2.12.0
[15] S4Vectors_0.16.0 Biobase_2.38.0
[17] oligoClasses_1.40.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.8.0 gtools_3.5.0 splines_3.4.3
[4] lattice_0.20-35 colorspace_1.3-2 blob_1.1.0
[7] rlang_0.1.4 bit64_0.9-7 affyio_1.48.0
[10] matrixStats_0.52.2 GenomeInfoDbData_1.0.0 foreach_1.4.4
[13] plyr_1.8.4 zlibbioc_1.24.0 munsell_0.4.3
[16] gtable_0.2.0 caTools_1.17.1 codetools_0.2-15
[19] memoise_1.1.0 labeling_0.3 ff_2.2-13
[22] GenomeInfoDb_1.14.0 preprocessCore_1.40.0 Rcpp_0.12.14
[25] KernSmooth_2.23-15 scales_0.5.0 gdata_2.18.0
[28] DelayedArray_0.4.1 affxparser_1.50.0 bit_1.1-12
[31] digest_0.6.13 GenomicRanges_1.30.0 grid_3.4.3
[34] tools_3.4.3 bitops_1.0-6 RCurl_1.95-4.8
[37] lazyeval_0.2.1 tibble_1.3.4 pkgconfig_2.0.1
[40] Matrix_1.2-12 iterators_1.0.9 compiler_3.4.3
Thank you!
And to be clear: