Skip to content

Latest commit

 

History

History
executable file
·
170 lines (109 loc) · 5.61 KB

cran-comments.md

File metadata and controls

executable file
·
170 lines (109 loc) · 5.61 KB
Raw

Resubmission

This is a resubmission. In my previous submission I asserted that

https://gatkforums.broadinstitute.org/gatk/discussion/6926/spanning-or-overlapping-deletions-allele

was a valid URL. However, CRAN correctly identified it as invalid. This has been updated to the following.

https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-

I have now also validated that

http://www.1000genomes.org/node/101 https://uswest.ensembl.org/info/docs/tools/vep/index.html

are valid URLs by pasting them into firefox.

Submission

This package, vcfR, was archived on CRAN on 2020-07-05 because CRAN asked me to address issues that I was unable to address before their deadline. This submission is in hope of being restored to CRAN. The issues I received via email are as follows.

checkbashisms is not even in SystemRequirements and used
unconditionally.  See 'Writing R Extensions', which called that 'annoying'.

It is a Debian script and not widely installed.

Your moniker "briank.lists" is not appropriate for a CRAN maintainer --
see the CRAN policy.

It appears that I misunderstood how to handle "checkbashisms." I posted on R-pkg-devel and was advised that I should assume that CRAN machines that require this script should have it. I have removed my "configure" script which attempted to handle this on my side.

I do not understand the criticism of my email or "moniker" of "[email protected]." I feel this is a misunderstanding. I have consulted the CRAN Repository Policy at the below link.

https://cran.r-project.org/web/packages/policies.html

It states that the maintainer must be "a person, not a mailing list" which I feel may be the source of the confusion. The address "[email protected]" is my personal address where I receive email from the various lists I subscribe to (and have been using since vcfR 1.0.0). It is not a mailing list. If I am mistaken please provide clarification. Thank you!

Test environments

  • local: ubuntu 18.04 LTS and R 4.0.2

  • local: OS X Catalina 10.15.6 and R 4.0.2 and clang

win-builder:

  • using R version 4.0.2 (2020-06-22)
  • using R Under development (unstable) (2020-08-23 r79071)

travis-ci:

  • Ubuntu 16.04.6 LTS, R version 4.0.0 (2020-04-24)
  • Ubuntu 16.04.6 LTS, R Under development (unstable) (2020-08-26 r79084)

Currently failing: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/travis/R/Library/ape/libs/ape.so': libRlapack.so: cannot open shared object file: No such file or directory

My interpretation is that this is not due to vcfR.

AppVeyor:

  • Windows Server 2012 R2 x64 (build 9600), R Under development (unstable) (2020-08-24 r79088)
  • Windows Server 2012 R2 x64 (build 9600), R version 4.0.2 (2020-06-22)

rhub:

  • None for this submission

R CMD check results

  • checking CRAN incoming feasibility ... NOTE Maintainer: 'Brian J. Knaus [email protected]'

New submission

Package was archived on CRAN

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

These words and acronyms are esoteric to working with genomic data and are all correctly spelled.

Found the following (possibly) invalid URLs: URL: https://uswest.ensembl.org/info/docs/tools/vep/index.html From: man/vep.Rd Status: Error Message: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate (Status without verification: OK) URL: https://www.internationalgenome.org/node/101 From: inst/doc/intro_to_vcfR.html Status: Error Message: libcurl error code 60: SSL certificate problem: unable to get local issuer certificate (Status without verification: OK)

These URLs all work when pasted into firefox.

  • checking installed package size ... NOTE installed size is 10.4Mb sub-directories of 1Mb or more: libs 8.5Mb

This has not been an issue in the past.

  • checking for future file timestamps ... NOTE unable to verify current time

I interpret this as not an issue with vcfR.

Thank you CRAN Core Team!

CRAN Repository Policy 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.

v1.12.0 Thank you Uwe Ligges for processing my submission!

v1.11.0 Thank you Uwe Ligges for processing my submission!

v1.10.0 Thank you Uwe Ligges for processing my submission!

v1.9.0 Thank you Uwe Ligges for processing my submission!

v1.8.0 Thank you Uwe Ligges for processing my submission!

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!

v1.4.0 Thank you Uwe Ligges and Kurt Hornik for helping me!

v1.3.0 Thank you Uwe Ligges and Kurt Hornik for helping me! Prof Brian Ripley brought to my attention that I had new memory access issues. Thank you again for bringing these to my attention!

v1.2.0 Thank you Uwe Ligges for helping me! This version was accepted on the first try. See Uwe, I'm learning!

Prof. Brian Ripley also brought to my attention that I had overlooked memory-access errors and that valgrind was reporting use of uninitialized memory and many small memory leaks. Thank you for bringing this to my attention, its a big help for those of us who are still learning valgrind!

v1.1.0 Thank you Uwe Ligges for helping me get my title in title case, my Description in order and handling my submission!