From 51f152cca4416c1e8238258225fb6d11b1deee6a Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Tue, 20 Feb 2018 06:40:29 +1100 Subject: [PATCH] Change the package path --- ROBITools/DESCRIPTION => DESCRIPTION | 0 ROBITools/LICENSE-SLRE => LICENSE-SLRE | 0 ROBITools/NAMESPACE => NAMESPACE | 0 {ROBITools/R => R}/02_class_metabarcoding.data.R | 0 {ROBITools/R => R}/ROBITools.R | 0 {ROBITools/R => R}/aggregate.R | 0 {ROBITools/R => R}/choose.taxonomy.R | 0 {ROBITools/R => R}/contaslayer.R | 0 {ROBITools/R => R}/distrib.extrapol.R | 0 {ROBITools/R => R}/experimental.section.R | 0 {ROBITools/R => R}/export-metabarcoding.R | 0 {ROBITools/R => R}/import.metabarcoding.R | 0 {ROBITools/R => R}/import.ngsfilter.R | 0 {ROBITools/R => R}/layers.metabarcoding.R | 0 {ROBITools/R => R}/metabarcoding_threshold.R | 0 {ROBITools/R => R}/mstat.R | 0 {ROBITools/R => R}/obiclean.R | 0 {ROBITools/R => R}/pcrslayer.R | 0 {ROBITools/R => R}/plot.PCRplate.R | 0 {ROBITools/R => R}/plot.seqinsample.R | 0 {ROBITools/R => R}/rarefy.R | 0 {ROBITools/R => R}/read.ngsfilter.R | 0 {ROBITools/R => R}/read.obitab.R | 0 {ROBITools/R => R}/read.sumatra.R | 0 {ROBITools/R => R}/s3objects.R | 0 {ROBITools/R => R}/taxoDBtree.R | 0 {ROBITools/R => R}/taxonomic.resolution.R | 0 {ROBITools/R => R}/taxonomy_classic_table.R | 0 ROBITools/README-SLRE.md => README-SLRE.md | 0 ROBITools/.gitignore | 3 --- {ROBITools/data => data}/termes.rda | Bin {ROBITools/inst => inst}/extdata/termes.fasta | 0 {ROBITools/inst => inst}/extdata/termes.tab | 0 {ROBITools/inst => inst}/extdata/termes_ngsfilt.txt | 0 {ROBITools/src => src}/ecoError.c | 0 {ROBITools/src => src}/ecoIOUtils.c | 0 {ROBITools/src => src}/ecoMalloc.c | 0 {ROBITools/src => src}/ecoPCR.h | 0 {ROBITools/src => src}/ecodna.c | 0 {ROBITools/src => src}/ecofilter.c | 0 {ROBITools/src => src}/econame.c | 0 {ROBITools/src => src}/ecorank.c | 0 {ROBITools/src => src}/ecoseq.c | 0 {ROBITools/src => src}/ecotax.c | 0 {ROBITools/src => src}/robitax.c | 0 {ROBITools/src => src}/robitax.h | 0 {ROBITools/src => src}/slre.c | 0 {ROBITools/src => src}/slre.h | 0 48 files changed, 3 deletions(-) rename ROBITools/DESCRIPTION => DESCRIPTION (100%) rename ROBITools/LICENSE-SLRE => LICENSE-SLRE (100%) rename ROBITools/NAMESPACE => NAMESPACE (100%) rename {ROBITools/R => R}/02_class_metabarcoding.data.R (100%) rename {ROBITools/R => R}/ROBITools.R (100%) rename {ROBITools/R => R}/aggregate.R (100%) rename {ROBITools/R => R}/choose.taxonomy.R (100%) rename {ROBITools/R => R}/contaslayer.R (100%) rename {ROBITools/R => R}/distrib.extrapol.R (100%) rename {ROBITools/R => R}/experimental.section.R (100%) rename {ROBITools/R => R}/export-metabarcoding.R (100%) rename {ROBITools/R => R}/import.metabarcoding.R (100%) rename {ROBITools/R => R}/import.ngsfilter.R (100%) rename {ROBITools/R => R}/layers.metabarcoding.R (100%) rename {ROBITools/R => R}/metabarcoding_threshold.R (100%) rename {ROBITools/R => R}/mstat.R (100%) rename {ROBITools/R => R}/obiclean.R (100%) rename {ROBITools/R => R}/pcrslayer.R (100%) rename {ROBITools/R => R}/plot.PCRplate.R (100%) rename {ROBITools/R => R}/plot.seqinsample.R (100%) rename {ROBITools/R => R}/rarefy.R (100%) rename {ROBITools/R => R}/read.ngsfilter.R (100%) rename {ROBITools/R => R}/read.obitab.R (100%) rename {ROBITools/R => R}/read.sumatra.R (100%) rename {ROBITools/R => R}/s3objects.R (100%) rename {ROBITools/R => R}/taxoDBtree.R (100%) rename {ROBITools/R => R}/taxonomic.resolution.R (100%) rename {ROBITools/R => R}/taxonomy_classic_table.R (100%) rename ROBITools/README-SLRE.md => README-SLRE.md (100%) delete mode 100644 ROBITools/.gitignore rename {ROBITools/data => data}/termes.rda (100%) rename {ROBITools/inst => inst}/extdata/termes.fasta (100%) rename {ROBITools/inst => inst}/extdata/termes.tab (100%) rename {ROBITools/inst => inst}/extdata/termes_ngsfilt.txt (100%) rename {ROBITools/src => src}/ecoError.c (100%) rename {ROBITools/src => src}/ecoIOUtils.c (100%) rename {ROBITools/src => src}/ecoMalloc.c (100%) rename {ROBITools/src => src}/ecoPCR.h (100%) rename {ROBITools/src => src}/ecodna.c (100%) rename {ROBITools/src => src}/ecofilter.c (100%) rename {ROBITools/src => src}/econame.c (100%) rename {ROBITools/src => src}/ecorank.c (100%) rename {ROBITools/src => src}/ecoseq.c (100%) rename {ROBITools/src => src}/ecotax.c (100%) rename {ROBITools/src => src}/robitax.c (100%) rename {ROBITools/src => src}/robitax.h (100%) rename {ROBITools/src => src}/slre.c (100%) rename {ROBITools/src => src}/slre.h (100%) diff --git a/ROBITools/DESCRIPTION b/DESCRIPTION similarity index 100% rename from ROBITools/DESCRIPTION rename to DESCRIPTION diff --git a/ROBITools/LICENSE-SLRE b/LICENSE-SLRE similarity index 100% rename from ROBITools/LICENSE-SLRE rename to LICENSE-SLRE diff --git a/ROBITools/NAMESPACE b/NAMESPACE similarity index 100% rename from ROBITools/NAMESPACE rename to NAMESPACE diff --git a/ROBITools/R/02_class_metabarcoding.data.R b/R/02_class_metabarcoding.data.R similarity index 100% rename from ROBITools/R/02_class_metabarcoding.data.R rename to R/02_class_metabarcoding.data.R diff --git a/ROBITools/R/ROBITools.R b/R/ROBITools.R similarity index 100% rename from ROBITools/R/ROBITools.R rename to R/ROBITools.R diff --git a/ROBITools/R/aggregate.R b/R/aggregate.R similarity index 100% rename from ROBITools/R/aggregate.R rename to R/aggregate.R diff --git a/ROBITools/R/choose.taxonomy.R b/R/choose.taxonomy.R similarity index 100% rename from ROBITools/R/choose.taxonomy.R rename to R/choose.taxonomy.R diff --git a/ROBITools/R/contaslayer.R b/R/contaslayer.R similarity index 100% rename from ROBITools/R/contaslayer.R rename to R/contaslayer.R diff --git a/ROBITools/R/distrib.extrapol.R b/R/distrib.extrapol.R similarity index 100% rename from ROBITools/R/distrib.extrapol.R rename to R/distrib.extrapol.R diff --git a/ROBITools/R/experimental.section.R b/R/experimental.section.R similarity index 100% rename from ROBITools/R/experimental.section.R rename to R/experimental.section.R diff --git a/ROBITools/R/export-metabarcoding.R b/R/export-metabarcoding.R similarity index 100% rename from ROBITools/R/export-metabarcoding.R rename to R/export-metabarcoding.R diff --git a/ROBITools/R/import.metabarcoding.R b/R/import.metabarcoding.R similarity index 100% rename from ROBITools/R/import.metabarcoding.R rename to R/import.metabarcoding.R diff --git a/ROBITools/R/import.ngsfilter.R b/R/import.ngsfilter.R similarity index 100% rename from ROBITools/R/import.ngsfilter.R rename to R/import.ngsfilter.R diff --git a/ROBITools/R/layers.metabarcoding.R b/R/layers.metabarcoding.R similarity index 100% rename from ROBITools/R/layers.metabarcoding.R rename to R/layers.metabarcoding.R diff --git a/ROBITools/R/metabarcoding_threshold.R b/R/metabarcoding_threshold.R similarity index 100% rename from ROBITools/R/metabarcoding_threshold.R rename to R/metabarcoding_threshold.R diff --git a/ROBITools/R/mstat.R b/R/mstat.R similarity index 100% rename from ROBITools/R/mstat.R rename to R/mstat.R diff --git a/ROBITools/R/obiclean.R b/R/obiclean.R similarity index 100% rename from ROBITools/R/obiclean.R rename to R/obiclean.R diff --git a/ROBITools/R/pcrslayer.R b/R/pcrslayer.R similarity index 100% rename from ROBITools/R/pcrslayer.R rename to R/pcrslayer.R diff --git a/ROBITools/R/plot.PCRplate.R b/R/plot.PCRplate.R similarity index 100% rename from ROBITools/R/plot.PCRplate.R rename to R/plot.PCRplate.R diff --git a/ROBITools/R/plot.seqinsample.R b/R/plot.seqinsample.R similarity index 100% rename from ROBITools/R/plot.seqinsample.R rename to R/plot.seqinsample.R diff --git a/ROBITools/R/rarefy.R b/R/rarefy.R similarity index 100% rename from ROBITools/R/rarefy.R rename to R/rarefy.R diff --git a/ROBITools/R/read.ngsfilter.R b/R/read.ngsfilter.R similarity index 100% rename from ROBITools/R/read.ngsfilter.R rename to R/read.ngsfilter.R diff --git a/ROBITools/R/read.obitab.R b/R/read.obitab.R similarity index 100% rename from ROBITools/R/read.obitab.R rename to R/read.obitab.R diff --git a/ROBITools/R/read.sumatra.R b/R/read.sumatra.R similarity index 100% rename from ROBITools/R/read.sumatra.R rename to R/read.sumatra.R diff --git a/ROBITools/R/s3objects.R b/R/s3objects.R similarity index 100% rename from ROBITools/R/s3objects.R rename to R/s3objects.R diff --git a/ROBITools/R/taxoDBtree.R b/R/taxoDBtree.R similarity index 100% rename from ROBITools/R/taxoDBtree.R rename to R/taxoDBtree.R diff --git a/ROBITools/R/taxonomic.resolution.R b/R/taxonomic.resolution.R similarity index 100% rename from ROBITools/R/taxonomic.resolution.R rename to R/taxonomic.resolution.R diff --git a/ROBITools/R/taxonomy_classic_table.R b/R/taxonomy_classic_table.R similarity index 100% rename from ROBITools/R/taxonomy_classic_table.R rename to R/taxonomy_classic_table.R diff --git a/ROBITools/README-SLRE.md b/README-SLRE.md similarity index 100% rename from ROBITools/README-SLRE.md rename to README-SLRE.md diff --git a/ROBITools/.gitignore b/ROBITools/.gitignore deleted file mode 100644 index bc1dd02..0000000 --- a/ROBITools/.gitignore +++ /dev/null @@ -1,3 +0,0 @@ -/man/ -/loopbenchmark.R -/Read-and-delete-me diff --git a/ROBITools/data/termes.rda b/data/termes.rda similarity index 100% rename from ROBITools/data/termes.rda rename to data/termes.rda diff --git a/ROBITools/inst/extdata/termes.fasta b/inst/extdata/termes.fasta similarity index 100% rename from ROBITools/inst/extdata/termes.fasta rename to inst/extdata/termes.fasta diff --git a/ROBITools/inst/extdata/termes.tab b/inst/extdata/termes.tab similarity index 100% rename from ROBITools/inst/extdata/termes.tab rename to inst/extdata/termes.tab diff --git a/ROBITools/inst/extdata/termes_ngsfilt.txt b/inst/extdata/termes_ngsfilt.txt similarity index 100% rename from ROBITools/inst/extdata/termes_ngsfilt.txt rename to inst/extdata/termes_ngsfilt.txt diff --git a/ROBITools/src/ecoError.c b/src/ecoError.c similarity index 100% rename from ROBITools/src/ecoError.c rename to src/ecoError.c diff --git a/ROBITools/src/ecoIOUtils.c b/src/ecoIOUtils.c similarity index 100% rename from ROBITools/src/ecoIOUtils.c rename to src/ecoIOUtils.c diff --git a/ROBITools/src/ecoMalloc.c b/src/ecoMalloc.c similarity index 100% rename from ROBITools/src/ecoMalloc.c rename to src/ecoMalloc.c diff --git a/ROBITools/src/ecoPCR.h b/src/ecoPCR.h similarity index 100% rename from ROBITools/src/ecoPCR.h rename to src/ecoPCR.h diff --git a/ROBITools/src/ecodna.c b/src/ecodna.c similarity index 100% rename from ROBITools/src/ecodna.c rename to src/ecodna.c diff --git a/ROBITools/src/ecofilter.c b/src/ecofilter.c similarity index 100% rename from ROBITools/src/ecofilter.c rename to src/ecofilter.c diff --git a/ROBITools/src/econame.c b/src/econame.c similarity index 100% rename from ROBITools/src/econame.c rename to src/econame.c diff --git a/ROBITools/src/ecorank.c b/src/ecorank.c similarity index 100% rename from ROBITools/src/ecorank.c rename to src/ecorank.c diff --git a/ROBITools/src/ecoseq.c b/src/ecoseq.c similarity index 100% rename from ROBITools/src/ecoseq.c rename to src/ecoseq.c diff --git a/ROBITools/src/ecotax.c b/src/ecotax.c similarity index 100% rename from ROBITools/src/ecotax.c rename to src/ecotax.c diff --git a/ROBITools/src/robitax.c b/src/robitax.c similarity index 100% rename from ROBITools/src/robitax.c rename to src/robitax.c diff --git a/ROBITools/src/robitax.h b/src/robitax.h similarity index 100% rename from ROBITools/src/robitax.h rename to src/robitax.h diff --git a/ROBITools/src/slre.c b/src/slre.c similarity index 100% rename from ROBITools/src/slre.c rename to src/slre.c diff --git a/ROBITools/src/slre.h b/src/slre.h similarity index 100% rename from ROBITools/src/slre.h rename to src/slre.h