URL updates for package check

lvclark · Nov 6, 2022 · 130a9b5 · 130a9b5
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diff --git a/man/exampleRAD.Rd b/man/exampleRAD.Rd
@@ -34,7 +34,7 @@ polyRAD/extdata/simulate_rad_data.R.
 
 \emph{M. sinensis} sequencing data available at
 \url{https://www.ncbi.nlm.nih.gov//bioproject/PRJNA207721}, with full genotype
-calls at \url{https://doi.org/10.13012/B2IDB-1402948_V1}.
+calls at \doi{10.13012/B2IDB-1402948_V1}.
 }
 
 \examples{

diff --git a/man/readTASSELGBSv2.Rd b/man/readTASSELGBSv2.Rd
@@ -64,9 +64,9 @@ the two input files.
 \references{
 TASSEL GBSv2 pipeline: \url{https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline}
 
-Bowtie2: \url{http://bowtie-bio.sourceforge.net/bowtie2/index.shtml}
+Bowtie2: \url{https://bowtie-bio.sourceforge.net/bowtie2/index.shtml}
 
-BWA: \url{http://bio-bwa.sourceforge.net/}
+BWA: \url{https://bio-bwa.sourceforge.net/}
 }
 \author{
 Lindsay V. Clark

diff --git a/vignettes/isolocus_sorting.Rmd b/vignettes/isolocus_sorting.Rmd
@@ -137,9 +137,9 @@ Depending on the complexity of your dataset, it can be quite a large file.
 
 Next, align the FASTQ file generated in step 2 of the previous section to your
 reference genome.  If you have never used
-[Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
+[Bowtie2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
 on your reference genome before, you will first need to
-[make an index](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer).
+[make an index](https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer).
 
 ```
 bowtie2-build Msinensis_497_v7.0.hardmasked.fa Msi_DH1_7