Merge remote-tracking branch 'upstream/master'

DESCRIPTION

@@ -8,7 +8,7 @@ Description: Facilitates easy manipulation of variant call format (VCF) data.
     data may be written to a VCF file (*.vcf.gz). It also may be converted into
     other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between
     VCF data and familiar R software.
-Version: 1.10.0
+Version: 1.12.0
 Authors@R: c(
     person(c("Brian", "J."), "Knaus", role = c("cre", "aut"),
     email = "[email protected]", comment = c(ORCID = "0000-0003-1665-4343")),
@@ -56,5 +56,5 @@ Suggests:
     tidyr
 VignetteBuilder: knitr
 License: GPL-3
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.1
 Encoding: UTF-8

NEWS.md

@@ -10,6 +10,18 @@ I think I encountered a situation where 4-96 was not enough so I've bumped it to
 This may have been addressed at 64a308ba50b9119108e8946737460de5997b805b by adding `samples` to vcfR method `[`.
 * In issue #92 (vcfR2genlight big data #92), JimWhiting91 has documented that `extract.gt()` could be greatly improved with multithreading. While he used `mclapply()` I do not feel this is the best solution because it does not work on Windows. I think a better solution would be [RCppParallel](https://rcppcore.github.io/RcppParallel/) because this should work on all CRAN platforms.
 
+# vcfR 1.13.0
+Released on CRAN 202X-XX-XX
+
+# vcfR 1.12.0
+Released on CRAN 2020-09-01
+* Added ```PKGTYPE: both``` to appveyor.yml so Windows packages can be built from source
+* Omitted ```configure``` file that unnecessarily tried to invoke checkbashisms
+* Incorporated help from https://stackoverflow.com/a/62721142 to use checkbashisms when checking on Debian flavors of Linux (ended up omitting this change but left this here to document it and the link)
+
+# vcfR 1.11.0
+Released on CRAN 2020-06-05
+* Now compatible with R 4.0.0 and dplyr 1.0.0
 
 # vcfR 1.10.0
 Released on CRAN 2020-02-06

R/vcfR2DNAbin.R

@@ -66,7 +66,7 @@
 #' 
 #' 
 #' When a variant overlaps a deletion it may be encoded by an \strong{asterisk allele (*)}.
-#' The GATK site covers this in a post on \href{https://gatkforums.broadinstitute.org/gatk/discussion/6926/spanning-or-overlapping-deletions-allele}{Spanning or overlapping deletions} ].
+#' The GATK site covers this in a post on \href{https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-}{Spanning or overlapping deletions} ].
 #' This is handled in vcfR by allowing the user to decide how it is handled with the paramenter \code{asterisk_as_del}.
 #' When \code{asterisk_as_del} is TRUE this allele is converted into a deletion ('-').
 #' When \code{asterisk_as_del} is FALSE the asterisk allele is converted to NA.

R/vcfR_to_tidy_functions.R

@@ -597,15 +597,15 @@ guess_types <- function(D) {
   tmp <- D %>%
 #    dplyr::filter_(~Number == 1) %>%
     dplyr::filter(Number == 1) %>%
-    dplyr::mutate(tt = ifelse(Type == "Integer", "i", ifelse(Type == "Numeric" | Type == "Float", "n", ""))) %>%
+    dplyr::mutate(tt = dplyr::if_else(Type == "Integer", "i", dplyr::if_else(Type == "Numeric" | Type == "Float", "n", ""))) %>%
     dplyr::filter(tt %in% c("n", "i")) %>%
 #    dplyr::filter_(~tt %in% c("n", "i")) %>%
     dplyr::select(ID, Number, Type, tt)
 #    dplyr::select_(~ID, ~Number, ~Type, ~tt)
 
 #  tmp <- D %>%  dplyr::filter_(~Number == 0 & Type == 'Flag')  %>%
   tmp <- D %>%  dplyr::filter(Number == 0 & Type == 'Flag')  %>%
-    dplyr::mutate(tt = ifelse(Type == "Flag", "f")) %>%
+    dplyr::mutate(tt = dplyr::if_else(Type == "Flag", "f", "")) %>%
     dplyr::filter(tt %in% c("f")) %>%
 #    dplyr::filter_(~tt %in% c("f")) %>%
     dplyr::select(ID, Number, Type, tt)  %>%

README.md

@@ -129,9 +129,9 @@ If you know of a software that I have not included on this list, particularly if
 
 * [Cortex](http://cortexassembler.sourceforge.net/)
 * [freebayes](https://github.com/ekg/freebayes)
-* [GATK haplotype caller](https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php)
-* [GATK MuTect2](https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php)
-* [GATK GenotypeGVCFs](https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php)
+* [GATK haplotype caller](https://software.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php)
+* [GATK MuTect2](https://software.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php)
+* [GATK GenotypeGVCFs](https://software.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php)
 * [LoFreq](http://csb5.github.io/lofreq/)
 * [Samtools](http://www.htslib.org/)
 * [VarScan2](http://dkoboldt.github.io/varscan/)
@@ -140,7 +140,7 @@ If you know of a software that I have not included on this list, particularly if
 **Restriction site associated DNA markers (e.g., RADseq, GBS):**
 
 * [Stacks](http://catchenlab.life.illinois.edu/stacks/)
-* [Tassel](http://www.maizegenetics.net/#!tassel/c17q9)
+* [Tassel](https://www.maizegenetics.net)
 
 **Manipulation of VCF data:**
 

appveyor.yml

@@ -18,6 +18,7 @@ cache:
 environment:
   global:
     WARNINGS_ARE_ERRORS: 1
+    PKGTYPE: both
 
   matrix:
     - R_VERSION: devel

cran-comments.md

@@ -1,80 +1,148 @@
 
-vcfR was last published on CRAN on 2020-01-10, so this may appear as an early resubmission.
-However, I was asked by CRAN to fix warnings occurring on R-devel by 2-17 so I'm submitting.
+
+## 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 16.04 LTS and R 3.6.2
-* local: OS X Catalina 10.15.2 and R 3.6.2 and clang
-* travis-ci: ubuntu 16.04 LTS, R 3.6.2 and R Under development (unstable) (2020-02-04 r77771)
-* AppVeyor: Windows Server 2012 R2 x64 (build 9600) R version 3.6.2 Patched (2020-01-25 r77764)
-* winbuilder: R version 3.6.2 (2019-12-12) and R Under development (unstable) (2020-01-28 r77738)
 
-## R CMD check results
-There were no ERRORs.
+* local:
+ubuntu 18.04 LTS and R 4.0.2
 
-There were 2 NOTEs:
+* local:
+OS X Catalina 10.15.6 and R 4.0.2 and clang
 
-Found the following (possibly) invalid URLs:
-  URL: http://www.1000genomes.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)
+win-builder:
+* using R version 4.0.2 (2020-06-22)
+* using R Under development (unstable) (2020-08-23 r79071)
 
-This url works when I copy and paste it into firefox.
+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)
 
-> checking installed package size ... NOTE
-    installed size is  9.9Mb
-    sub-directories of 1Mb or more:
-      libs   8.0Mb
+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
 
-## Downstream dependencies
+My interpretation is that this is not due to vcfR.
 
-I have also run R CMD check on downstream dependencies of vcfR
-All packages that I could install passed:
+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)
 
-devtools::revdep_check() is no longer a part of devtools and the package revdepcheck (on GitHub but not CRAN) threw an error because a dependent R package could not be installed.
+rhub:
+* None for this submission
+
+
+## R CMD check results
 
-I used:
-R CMD check --as-cran
-on the tarballs from CRAN for the following packages.
+* checking CRAN incoming feasibility ... NOTE
+Maintainer: 'Brian J. Knaus <[email protected]>'
 
-Reverse imports: 	binmapr, pcadapt, whoa
-Reverse suggests: 	LDheatmap, onemap, perfectphyloR, rehh, SimRVSequences
+New submission
 
-I spent an entire afternoon trying to install dependencies of reversedependencies of vcfR but was not successful.
-It appears there are dependencies of these packages that are not available for R version 3.6.2.
+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.
 
-Results:
 
-WARNINGS were thrown because the version tested was the same as on CRAN.
+* checking installed package size ... NOTE
+  installed size is 10.4Mb
+  sub-directories of 1Mb or more:
+    libs   8.5Mb
 
-binmapr
-* checking Rd cross-references ... NOTE
-Package unavailable to check Rd xrefs: ‘qtl’
+This has not been an issue in the past.
 
-pcadapt
-* checking package dependencies ... ERROR
-Packages required but not available:
-  'mmapcharr', 'plotly', 'robust', 'RSpectra', 'rmio'
 
-These do not appear to be available for R version 3.6.2.
+* checking for future file timestamps ... NOTE
+unable to verify current time
 
-LDheatmap
-Warning message:
-package ‘snpStats’ is not available (for R version 3.6.2) 
+I interpret this as not an issue with vcfR.
 
-onemap
-package ‘MDSmap’ is not available (for R version 3.6.2)
 
 ## 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.
 
+v1.12.0 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!

vignettes/intro_to_vcfR.Rmd

@@ -41,7 +41,7 @@ This is one situation where not having complete chromosomes actually can be an a
 ## Data input
 
 
-The vcfR package is designed to work with data from [VCF](http://www.1000genomes.org/node/101) files.
+The vcfR package is designed to work with data from [VCF](https://www.internationalgenome.org/node/101) files.
 The use of a sequence file ([FASTA format](https://en.wikipedia.org/wiki/FASTA_format)) and an annotation file ([GFF format](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)) can provide helpful context, but are not required.
 We'll begin our example by locating the data files from the package 'pinfsc50.'