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CRAN 1.7.0 version
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knausb committed Feb 8, 2018
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2 changes: 1 addition & 1 deletion NEWS.md
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Expand Up @@ -9,7 +9,7 @@ This may have been addressed at 64a308ba50b9119108e8946737460de5997b805b by addi


# vcfR 1.7.0
Released on CRAN 2018-02-XX.
Released on CRAN 2018-02-07.
* `vcf_field_names()` now delimts on KEY= of key/value pairs, allows commas to be used within value.
* `read.vcfR()` will download files when provided with a link.
* Added example data from the Variant Effect Predictor (vep) `data(vep)`.
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36 changes: 18 additions & 18 deletions cran-comments.md
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## Test environments
* local: ubuntu 16.04 LTS, R 3.4.3
* local: OS X install, R 3.4.2 (binaries for OSX 3.4.3 do not appear available yet)
* local: OS X install, R 3.4.3
* ubuntu 14.04.5 LTS (on travis-ci), R 3.4.2
* Windows Server 2012 R2 x64 (build 9600; on AppVeyor), R version 3.4.3 Patched (2018-02-03 r74215)
* winbuilder: R version 3.4.3 (2017-11-30)
* winbuilder: R Under development (unstable) (2017-09-12 r73242)
* winbuilder: R Under development (unstable) (2018-02-01 r74194)


## R CMD check results
Expand All @@ -18,47 +18,47 @@ There was 1 NOTE:
Maintainer: ‘Brian J. Knaus <[email protected]>’

* checking installed package size ... NOTE
installed size is 8.6Mb
installed size is 9.5Mb
sub-directories of 1Mb or more:
doc 3.0Mb
libs 5.7Mb


There are 4 vignettes (HTML) which contribute to the 2.8Mb in doc.
These could be migrated to a separate documentation package.
This could reduce this package's size.
Because this is a NOTE and not an ERROR or WARNING I have left it as one package for now.
libs 7.8Mb


Possibly mis-spelled words in DESCRIPTION:
DNAbin (9:76)
VCF (2:33, 3:68, 4:62, 5:10, 8:58, 10:34)
VcfR (10:5)
genlight (9:66)
genomic (7:51)
DNAbin (9:46)
VCF (2:33, 3:68, 4:62, 5:5, 8:30, 10:5)
VcfR (9:55)
genlight (9:36)

I have reviewed these words and feel they are spelled correctly.
'DNAbin' refers to an object of class ape::DNAbin.
'VCF' refers to the variant call format specification, a format of file handled by this package.
'VcfR' refers to this package.
'genlight' refers to an object of class adegenet::genlight.
'genomic' refers to properties of a genome.


## Downstream dependencies

I have also run R CMD check on downstream dependencies of vcfR
All packages that I could install passed:

* pcadapt: no errors or warnings
devtools::revdep_check()

Checked annovarR: 1 error | 0 warnings | 0 notes
Checked pcadapt : 0 errors | 0 warnings | 3 notes

The ERROR from annovarR is below, I do not feel this is related to vcfR.

ERROR: dependencies ‘RMySQL’, ‘AnnotationDbi’ are not available for package ‘annovarR’
* removing ‘/tmp/Rtmp4bz1PA/R-lib/annovarR’

## Thank you CRAN Core Team!

[CRAN Repository Policy](https://cran.r-project.org/web/packages/policies.html) states that all correspondence should be with CRAN and not members of the team.
However, I think its polite to thank those who have helped this project.
So I've decided to start a list of thanks with the hope that these individuals may see this in the future.

v1.7.0 Thank you Uwe Ligges for processing my submission!

v1.6.0 Thank you Uwe Ligges for processing my submission!

v1.5.0 Thank you Kurt Hornik for helping me!
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