Hi,
I found a NAMESPACE issue in bumphunter version 1.11.3 as reported at
https://github.com/ririzarr/bumphunter/issues/7 with the proposed fix
at
https://github.com/lcolladotor/bumphunter/commit/4093a628ecd81ace3a26511b82d2c3ca47849d33
However the bumphunter GitHub repository is outdated versus the
version available in Bioc-devel as I reported at
https://github.com/ririzarr/bumphunter/issues/9. I can recognize that
it stopped being in sync once the git-svn-bridge stopped working.
Which is why I'm sending here a SVN diff file with the patch that can
fix this small issue.
The patch reads:
Index: DESCRIPTION
===================================================================
--- DESCRIPTION (revision 115247)
+++ DESCRIPTION (working copy)
@@ -1,5 +1,5 @@
Package: bumphunter
-Version: 1.11.3
+Version: 1.11.4
Title: Bump Hunter
Description: Tools for finding bumps in genomic data
Authors@R: c(person(c("Rafael", "A."), "Irizarry", role = c("cre","aut"), email
Index: NAMESPACE
===================================================================
--- NAMESPACE (revision 115247)
+++ NAMESPACE (working copy)
@@ -19,6 +19,7 @@
importFrom(GenomicRanges, GRanges, makeGRangesFromDataFrame)
importMethodsFrom(GenomicRanges, sort)
importFrom(locfit, locfit)
+importFrom(locfit, lp)
importFrom(utils, data, packageDescription)
importFrom(parallel, mclapply, stopCluster)
importFrom(GenomicFeatures, exonsBy, cdsBy, transcriptsBy)
Best,
Leonardo
Leonardo Collado Torres, PhD Candidate
Department of Biostatistics
Johns Hopkins University
Bloomberg School of Public Health
Website: http://lcolladotor.github.io/about.html
Index: DESCRIPTION
===================================================================
--- DESCRIPTION (revision 115247)
+++ DESCRIPTION (working copy)
@@ -1,5 +1,5 @@
Package: bumphunter
-Version: 1.11.3
+Version: 1.11.4
Title: Bump Hunter
Description: Tools for finding bumps in genomic data
Authors@R: c(person(c("Rafael", "A."), "Irizarry", role = c("cre","aut"), email
Index: NAMESPACE
===================================================================
--- NAMESPACE (revision 115247)
+++ NAMESPACE (working copy)
@@ -19,6 +19,7 @@
importFrom(GenomicRanges, GRanges, makeGRangesFromDataFrame)
importMethodsFrom(GenomicRanges, sort)
importFrom(locfit, locfit)
+importFrom(locfit, lp)
importFrom(utils, data, packageDescription)
importFrom(parallel, mclapply, stopCluster)
importFrom(GenomicFeatures, exonsBy, cdsBy, transcriptsBy)
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