Hi Kasper,
Your tutorials on Bioc have been outstanding. Thank you very much for your tremendous contributions to the online community of learners such as myself.
It appears that in the more recent versions of GenomeInfoDb the keepSeqlevels, dropSeqlevels, and keepStandardChromosomes commands in the script "GenomicRanges_seqinfo.R" throw errors as they require an argument "pruning.mode='coarse'" to be passed.
Here is my session info:
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 base
other attached packages:
[1] GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 IRanges_2.12.0 S4Vectors_0.16.0 AnnotationHub_2.10.1
[6] BiocGenerics_0.24.0 BiocInstaller_1.28.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 AnnotationDbi_1.40.0 XVector_0.18.0 magrittr_1.5
[5] zlibbioc_1.24.0 bit_1.1-14 xtable_1.8-2 R6_2.2.2
[9] blob_1.1.1 httr_1.3.1 tools_3.4.3 Biobase_2.38.0
[13] DBI_1.0.0 htmltools_0.3.6 yaml_2.1.19 bit64_0.9-7
[17] digest_0.6.15 interactiveDisplayBase_1.16.0 GenomeInfoDbData_1.0.0 shiny_1.1.0
[21] later_0.7.3 bitops_1.0-6 promises_1.0.1 RCurl_1.95-4.10
[25] curl_3.2 memoise_1.1.0 RSQLite_2.1.1 mime_0.5
[29] compiler_3.4.3 httpuv_1.4.4.1 pkgconfig_2.0.1
-Vivek
Hi Kasper,
Your tutorials on Bioc have been outstanding. Thank you very much for your tremendous contributions to the online community of learners such as myself.
It appears that in the more recent versions of GenomeInfoDb the keepSeqlevels, dropSeqlevels, and keepStandardChromosomes commands in the script "GenomicRanges_seqinfo.R" throw errors as they require an argument "pruning.mode='coarse'" to be passed.
Here is my session info:
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 base
other attached packages:
[1] GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 IRanges_2.12.0 S4Vectors_0.16.0 AnnotationHub_2.10.1
[6] BiocGenerics_0.24.0 BiocInstaller_1.28.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 AnnotationDbi_1.40.0 XVector_0.18.0 magrittr_1.5
[5] zlibbioc_1.24.0 bit_1.1-14 xtable_1.8-2 R6_2.2.2
[9] blob_1.1.1 httr_1.3.1 tools_3.4.3 Biobase_2.38.0
[13] DBI_1.0.0 htmltools_0.3.6 yaml_2.1.19 bit64_0.9-7
[17] digest_0.6.15 interactiveDisplayBase_1.16.0 GenomeInfoDbData_1.0.0 shiny_1.1.0
[21] later_0.7.3 bitops_1.0-6 promises_1.0.1 RCurl_1.95-4.10
[25] curl_3.2 memoise_1.1.0 RSQLite_2.1.1 mime_0.5
[29] compiler_3.4.3 httpuv_1.4.4.1 pkgconfig_2.0.1
-Vivek