updated cran-comments.md for submission

cran-comments.md

@@ -1,5 +1,35 @@
 
-This release includes updates to address requests from CRAN to incorporate checkbashisms on Debian flavors or Linux.
+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
 
@@ -11,44 +41,40 @@ 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) (2020-07-19 r78884)
+* using R Under development (unstable) (2020-08-23 r79071)
 
 travis-ci:
-* ubuntu 16.04 LTS, R version 4.0.0 (2020-04-24)
-* ubuntu 16.04 LTS, R Under development (unstable) (2020-07-23 r78905)
+* 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)
 
 AppVeyor:
-* Windows Server 2012 R2 x64 (build 9600) R version 3.6.2 Patched (2020-01-25 r77764)
+* Windows Server 2012 R2 x64 (build 9600), R Under development (unstable) (2020-08-24 r79074)
 
-rhub:
+Error: (converted from warning) package 'utf8' is not available (as a binary package for R Under development
 
+I interpret this as not a vcfR issue.
 
+rhub:
+* None for this submission
 
-Issues:
+
+## R CMD check results
 
 * checking CRAN incoming feasibility ... NOTE
-Maintainer: ‘Brian J. Knaus <[email protected]>’
+Maintainer: 'Brian J. Knaus <[email protected]>'
 
 New submission
 
 Package was archived on CRAN
 
-Found the following (possibly) invalid URLs:
-  URL: https://gatkforums.broadinstitute.org/gatk/discussion/6926/spanning-or-overlapping-deletions-allele
-    From: man/vcfR2DNAbin.Rd
-    Status: Error
-    Message: libcurl error code 6:
-      	Could not resolve host: gatkforums.broadinstitute.org
-
-
-
-
-
-## R CMD check results
-There were no ERRORs.
+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.
 
-There were 2 NOTEs:
 
 Found the following (possibly) invalid URLs:
   URL: http://www.1000genomes.org/node/101
@@ -57,22 +83,33 @@ Found the following (possibly) invalid URLs:
     Message: libcurl error code 60:
       	SSL certificate problem: unable to get local issuer certificate
       	(Status without verification: OK)
+  URL: https://gatkforums.broadinstitute.org/gatk/discussion/6926/spanning-or-overlapping-deletions-allele
+    From: man/vcfR2DNAbin.Rd
+    Status: Error
+    Message: libcurl error code 6:
+      	Could not resolve host: gatkforums.broadinstitute.org
   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)
-      	
-This url works when I copy and paste it into firefox.
+
+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!