v1.17.2 -- Adds supported for TxDb objects with gene ids from ENSEMBL/GENCODE

[lcolladotor]

This commit resolves https://github.com/rafalab/bumphunter/issues/15 by adding the arguments mappingInfo and simplifyGeneID to annotateTranscripts(). mappingInfo is a named list whose elements are passed to AnnotateDbi::mapIds() for more flexible gene id matching between a given TxDb object and the organism package (like org.Hs.eg.db). simplifyGeneId is a logical and if TRUE gene ids like ENSTsomething.8_etc get simplified to ENSTsomething. This allows working with TxDb objects created from GENCODE GTF files and matching then to org.Hs.eg.db as if the ids were ENSEMBL gene ids.

A unit test checking the new changes has been added as well.

A check and build reveals no new notes/warnings/errors.

$ R CMD build --keep-empty-dirs --no-resave-data bumphunter
Loading required package: colorout
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* preparing ‘bumphunter’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘bumphunter_1.17.2.tar.gz’

$ R CMD check --no-vignettes --timings bumphunter_1.17.2.tar.gz
Loading required package: colorout
* using log directory ‘/Users/lcollado/Dropbox/Code/bumphunter.Rcheck’
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.17.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘foreach’
  ‘iterators’ ‘parallel’ ‘locfit’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bumphunter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bumphunterEngine: no visible binding for global variable ‘bootstraps’
Undefined global functions or variables:
  bootstraps
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/lcollado/Dropbox/Code/bumphunter.Rcheck/00check.log’
for details.

[lcolladotor]

Thanks @sampoll!

I guess that the next step is to git cherry-pick commits https://github.com/rafalab/bumphunter/commit/718d3d87af114f8dc404c3889c673fac861bb84c through https://github.com/rafalab/bumphunter/commit/8ae30a7daddec1b7e70d789cebb43f195a537a35 to Bioconductor. Then https://github.com/Bioconductor-mirror/bumphunter/commits/master would be updated.

In your local clone of rafalab/bumphunter, you'll have to run the update_remotes.sh script (see http://www.bioconductor.org/developers/how-to/git-mirrors/ for details). That will create a devel branch locally. Basically, from scratch it would be something like this (assuming you have git-svn installed):

git clone https://github.com/rafalab/bumphunter.git
curl -O https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh
cd bumphunter
bash ../update_remotes.sh
## See all the branches
git branch
git checkout devel
git cherry-pick 718d3d..8ae30a7

## You'll need svn write permissions for the bumphunter package to do this (and a svn passwd).
## Rafa can request Bioc to give them to you. I believe that you'll need to add yourself
## to the DESCRIPTION file as a maintainer. Talk about this with Rafa.
git svn dcommit

## After a couple of seconds you can update your local clone
git pull

## And return to the master branch
git checkout master

The git cherry-pick step might be a bit more complicated than what I posted.

Best, Leo

[sampoll]

I'm working on it. I need to be sure I know what I'm doing, because I definitely don't want to mangle Bioconductor's subversion repository. I think that would make me very unpopular with Bioconductor.

• Sam

On 5/10/17 9:51 AM, Leonardo Collado-Torres wrote:

Thanks @sampoll https://github.com/sampoll!

I guess that the next step is to |git cherry-pick| commits rafalab/bumphunter@718d3d8 https://github.com/rafalab/bumphunter/commit/718d3d87af114f8dc404c3889c673fac861bb84c through rafalab/bumphunter@8ae30a7 https://github.com/rafalab/bumphunter/commit/8ae30a7daddec1b7e70d789cebb43f195a537a35 to Bioconductor. Then https://github.com/Bioconductor-mirror/bumphunter/commits/master would be updated.

In your local clone of rafalab/bumphunter, you'll have to run the |update_remotes.sh| script (see http://www.bioconductor.org/developers/how-to/git-mirrors/ for details). That will create a |devel| branch locally. Basically, from scratch it would be something like this (assuming you have |git-svn| installed):

|git clone https://github.com/rafalab/bumphunter.git curl -O https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh cd bumphunter bash ../update_remotes.sh ## See all the branches git branch git checkout devel git cherry-pick 718d3d..8ae30a7 ## You'll need svn write permissions for the bumphunter package to do this (and a svn passwd). ## Rafa can request Bioc to give them to you. I believe that you'll need to add yourself ## to the DESCRIPTION file as a maintainer. Talk about this with Rafa. git svn dcommit ## After a couple of seconds you can update your local clone git pull ## And return to the master branch git checkout master |

The |git cherry-pick| step might be a bit more complicated than what I posted.

Best, Leo

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