# try to fix

DESCRIPTION

@@ -30,7 +30,6 @@ Imports:
   parallel,
   readr,
   rlang,
-  seqinr,
   stats,
   stringr,
   tidyr,
@@ -40,6 +39,7 @@ Suggests:
   rmarkdown,
   knitr,
   devtools,
+  seqinr,
   stringi,
   testthat,
   tibble
@@ -59,4 +59,4 @@ URL:
   https://gitlab.gwdg.de/mpievolbio-it/crbhits,
   https://mpievolbio-it.pages.gwdg.de/crbhits/
 BugReports: https://gitlab.gwdg.de/mpievolbio-it/crbhits/issues
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

R/filter_alnlen.R

@@ -25,9 +25,9 @@ filter_alnlen <- function(rbh,
     alignment_length <- NULL
     if(inverse){
         #return(rbh[as.numeric(rbh[,4])<alnlen, , drop=FALSE])
-        return(dplyr::filter(rbh, alignment_length<alnlen))
+        return(dplyr::filter(rbh, .data$alignment_length<alnlen))
     } else {
         #return(rbh[as.numeric(rbh[,4])>=alnlen, , drop=FALSE])
-        return(dplyr::filter(rbh, alignment_length>=alnlen))
+        return(dplyr::filter(rbh, .data$alignment_length>=alnlen))
     }
 }

R/filter_eval.R

@@ -25,9 +25,9 @@ filter_eval <- function(rbh,
     evalue <- NULL
     if(inverse){
         #return(rbh[as.numeric(rbh[,11])>evalue, , drop=FALSE])
-        return(dplyr::filter(rbh, evalue>eval))
+        return(dplyr::filter(rbh, .data$evalue>eval))
     } else {
         #return(rbh[as.numeric(rbh[,11])<=evalue, , drop=FALSE])
-        return(dplyr::filter(rbh, evalue<=eval))
+        return(dplyr::filter(rbh, .data$evalue<=eval))
     }
 }

R/filter_pident.R

@@ -25,9 +25,9 @@ filter_pident <- function(rbh,
     perc_identity <- NULL
     if(inverse){
         #return(rbh[as.numeric(rbh[,3])<pident, , drop=FALSE])
-        return(dplyr::filter(rbh, perc_identity<pident))
+        return(dplyr::filter(rbh, .data$perc_identity<pident))
     } else {
         #return(rbh[as.numeric(rbh[,3])>=pident, , drop=FALSE])
-        return(dplyr::filter(rbh, perc_identity>=pident))
+        return(dplyr::filter(rbh, .data$perc_identity>=pident))
     }
 }

R/filter_qcov.R

@@ -27,10 +27,12 @@ filter_qcov <- function(rbh,
     if(inverse){
         #return(rbh[(as.numeric(rbh[,4])/as.numeric(rbh[,13]))<qcov, ,
         #drop=FALSE])
-        return(dplyr::filter(rbh, (alignment_length / query_length)<qcov))
+        return(dplyr::filter(rbh, (.data$alignment_length /
+            .data$query_length)<qcov))
     } else {
         #return(rbh[(as.numeric(rbh[,4])/as.numeric(rbh[,13]))>=qcov, ,
         #drop=FALSE])
-        return(dplyr::filter(rbh, (alignment_length / query_length)>=qcov))
+        return(dplyr::filter(rbh, (.data$alignment_length /
+            .data$query_length)>=qcov))
     }
 }

R/filter_rost1999.R

@@ -32,11 +32,13 @@ filter_rost1999 <- function(rbh,
     #pident_by_length <- get_pident_by_length(as.numeric(rbh[, 4]))
     if(inverse){
         return(dplyr::filter(
-            rbh, perc_identity<get_pident_by_length(alignment_length)))
+            rbh, .data$perc_identity<
+            get_pident_by_length(.data$alignment_length)))
         #return(rbh[as.numeric(rbh[, 3])<pident_by_length, , drop=FALSE])
     } else {
         #return(rbh[as.numeric(rbh[, 3])>=pident_by_length, , drop=FALSE])
         return(dplyr::filter(
-            rbh, perc_identity>=get_pident_by_length(alignment_length)))
+            rbh, .data$perc_identity>=
+            get_pident_by_length(.data$alignment_length)))
     }
 }

R/filter_tcov.R

@@ -27,10 +27,12 @@ filter_tcov <- function(rbh,
     if(inverse){
         #return(rbh[(as.numeric(rbh[,4])/as.numeric(rbh[,14]))<tcov, ,
         #drop=FALSE])
-        return(dplyr::filter(rbh, (alignment_length / subject_length)<tcov))
+        return(dplyr::filter(rbh, (.data$alignment_length /
+            .data$subject_length)<tcov))
     } else {
         #return(rbh[(as.numeric(rbh[,4])/as.numeric(rbh[,14]))>=tcov, ,
         #drop=FALSE])
-        return(dplyr::filter(rbh, (alignment_length / subject_length)>=tcov))
+        return(dplyr::filter(rbh, (.data$alignment_length /
+            .data$subject_length)>=tcov))
     }
 }

R/gff2longest.R

@@ -84,6 +84,8 @@ gff2longest <- function(gff3file,
     transcriptID <- NULL
     transcriptLENGTH <- NULL
     mid <- NULL
+    proteinID <- NULL
+    dbxref_geneID <- NULL
     if(source=="NCBI"){
         gff3 <- readr::read_tsv(gff3file, col_names = FALSE, comment = "#")
         colnames(gff3) <- c("seqname", "source", "feature", "start", "end",

inst/extdata/maf-convert-crbhits

@@ -1,4 +1,4 @@
-#! /usr/bin/env python
+#! /usr/bin/env python3
 # Copyright 2010, 2011, 2013, 2014 Martin C. Frith
 # SPDX-License-Identifier: GPL-3.0-or-later
 # Seems to work with Python 2.x, x>=6