Prevent files cluttering package check folder

R/dataimport.R

@@ -235,8 +235,9 @@ read.SPAGeDi<-function(infile, allelesep="/", returnspatcoord=FALSE){
     }
 
     # read the rest of the file as a table
-    cat(Lines[3:(3+numind)], sep="\n", file="SpagTemp.txt")
-    gentable <- read.table("SpagTemp.txt", sep="\t", header=TRUE,
+    tmp <- tempfile()
+    cat(Lines[3:(3+numind)], sep="\n", file=tmp)
+    gentable <- read.table(tmp, sep="\t", header=TRUE,
                            row.names=1,
                            colClasses=c("character",rep(NA,catpres+numsc),
                            rep("character",numloc)))

man/read.ATetra.Rd

@@ -48,6 +48,8 @@ Lindsay V. Clark
 \examples{
 # create a file to be read
 # (this would normally be done in a text editor or with ATetra's Excel template)
+myfile <- tempfile()
+
 cat("TIT,Sample Rubus Data for ATetra", "LOC,1,CBA15",
 "POP,1,1,Commonwealth", "IND,1,1,1,CMW1,197,208,211,213",
 "IND,1,1,2,CMW2,197,207,211,212", "IND,1,1,3,CMW3,197,208,212,219",
@@ -62,10 +64,10 @@ cat("TIT,Sample Rubus Data for ATetra", "LOC,1,CBA15",
 "IND,2,2,6,FCR4,98,125,,","IND,2,2,7,FCR7,98,106,126,",
 "IND,2,2,8,FCR14,98,127,,","IND,2,2,9,FCR15,98,108,117,",
 "IND,2,2,10,FCR16,98,125,,","IND,2,2,11,FCR17,98,126,,","END",
-file = "atetraexample.txt", sep = "\n")
+file = myfile, sep = "\n")
 
 # Read the file and examine the data
-exampledata <- read.ATetra("atetraexample.txt")
+exampledata <- read.ATetra(myfile)
 summary(exampledata)
 PopNames(exampledata)
 viewGenotypes(exampledata)

man/read.GeneMapper.Rd

@@ -113,11 +113,12 @@ gentable <- data.frame(Sample.Name=rep(c("ind1","ind2","ind3"),2),
                        )
 # create a file (inspect this file in a text editor or spreadsheet
 # software to see the required format)
-write.table(gentable, file="readGMtest.txt", quote=FALSE, sep="\t",
+myfile <- tempfile()
+write.table(gentable, file=myfile, quote=FALSE, sep="\t",
             na="", row.names=FALSE, col.names=TRUE)
 
 # read the file
-mygenotypes <- read.GeneMapper("readGMtest.txt")
+mygenotypes <- read.GeneMapper(myfile)
 
 # inspect the results
 viewGenotypes(mygenotypes)

man/read.GenoDive.Rd

@@ -73,14 +73,15 @@ Lindsay V. Clark
 }
 \examples{
 # create data file (normally done in a text editor or spreadsheet software)
+myfile <- tempfile()
 cat(c("example comment line", "5\t2\t2\t3\t2", "pop1", "pop2",
       "pop\tind\tloc1\tloc2", "1\tJohn\t102\t1214",
       "1\tPaul\t202\t0", "2\tGeorge\t101\t121213",
       "2\tRingo\t10304\t131414","1\tYoko\t10303\t120014"),
-    file = "genodiveExample.txt", sep = "\n")
+    file = myfile, sep = "\n")
 
 # import file data
-exampledata <- read.GenoDive("genodiveExample.txt")
+exampledata <- read.GenoDive(myfile)
 
 # view data
 summary(exampledata)

man/read.POPDIST.Rd

@@ -72,6 +72,7 @@ Lindsay V. Clark
 }
 \examples{
 # Create a file to read (this is typically done in a text editor)
+myfile <- tempfile()
 cat("An example for the read.POPDIST documentation.",
 "abcR",
 "abcQ",
@@ -86,13 +87,13 @@ cat("An example for the read.POPDIST documentation.",
 "Great Works\t, 050807 030800",
 "Great Works\t, 0000 0408",
 "Great Works\t, 0707 0305",
-file="testPOPDIST.txt", sep="\n")
+file=myfile, sep="\n")
 
 # View the file in the R console (or open it in a text editor)
-cat(readLines("testPOPDIST.txt"), sep="\n")
+cat(readLines(myfile), sep="\n")
 
 # Read the file into a "genambig" object
-fishes <- read.POPDIST("testPOPDIST.txt")
+fishes <- read.POPDIST(myfile)
 
 # View the data in the object
 summary(fishes)

man/read.SPAGeDi.Rd

@@ -102,6 +102,7 @@ Lindsay V. Clark
 \examples{
 # create a file to read (usually done with spreadsheet software or a
 # text editor):
+myfile <- tempfile()
 cat("// here's a comment line at the beginning of the file",
 "5\t0\t-2\t2\t2\t4",
 "4\t5\t10\t50\t100",
@@ -112,13 +113,13 @@ cat("// here's a comment line at the beginning of the file",
 "ind4\t38.2\t-120.3\t00000000\t41430000",
 "ind5\t38.2\t-120.3\t00053137\t00414200",
 "END",
-sep="\n", file="SpagInputExample.txt")
+sep="\n", file=myfile)
 
 # display the file
-cat(readLines("SpagInputExample.txt"), sep="\n")
+cat(readLines(myfile), sep="\n")
 
 # read the file
-mydata <- read.SPAGeDi("SpagInputExample.txt", allelesep = "",
+mydata <- read.SPAGeDi(myfile, allelesep = "",
 returnspatcoord = TRUE)
 
 # view the data

man/read.STRand.Rd

@@ -68,19 +68,20 @@ strtemp <- data.frame(Pop=c("P1","P1","P2","P2"),
                       Ind=c("a","b","a","b"),
                       LocD=c("0","172/174","170/172/178*","172/176"),
                       LocG=c("130/136/138/142*","132/136","138","132/140/144*"))
-write.table(strtemp, file="strtemp.txt", sep="\t",
+myfile <- tempfile()
+write.table(strtemp, file=myfile, sep="\t",
             row.names=FALSE, quote=FALSE)
 
 # read the file
-mydata <- read.STRand("strtemp.txt")
+mydata <- read.STRand(myfile)
 viewGenotypes(mydata)
 PopNames(mydata)
 
 # alternative example with popInSam=FALSE
 strtemp$Ind <- c("OH1","OH5","MT4","MT7")
-write.table(strtemp, file="strtemp.txt", sep="\t",
+write.table(strtemp, file=myfile, sep="\t",
             row.names=FALSE, quote=FALSE)
-mydata <- read.STRand("strtemp.txt", popInSam=FALSE)
+mydata <- read.STRand(myfile, popInSam=FALSE)
 Samples(mydata)
 PopNames(mydata)
 }

man/read.Structure.Rd

@@ -134,6 +134,7 @@ Lindsay V. Clark
 \examples{
 # create a file to read (normally done in a text editor or spreadsheet
 # software)
+myfile <- tempfile()
 cat("\t\tRhCBA15\tRhCBA23\tRhCBA28\tRhCBA14\tRUB126\tRUB262\tRhCBA6\tRUB26",
     "\t\t-9\t-9\t-9\t-9\t-9\t-9\t-9\t-9",
     "WIN1B\t1\t197\t98\t152\t170\t136\t208\t151\t99",
@@ -168,13 +169,13 @@ cat("\t\tRhCBA15\tRhCBA23\tRhCBA28\tRhCBA14\tRUB126\tRUB262\tRhCBA6\tRUB26",
     "MCD3\t2\t-9\t-9\t-9\t-9\t-9\t-9\t-9\t-9",
     "MCD3\t2\t-9\t-9\t-9\t-9\t-9\t-9\t-9\t-9",
     "MCD3\t2\t-9\t-9\t-9\t-9\t-9\t-9\t-9\t-9",
-    sep="\n",file="structtest.txt")
+    sep="\n",file=myfile)
 
 # view the file
-cat(readLines("structtest.txt"), sep="\n")
+cat(readLines(myfile), sep="\n")
 
 # read the structure file into genotypes and populations
-testdata <- read.Structure("structtest.txt", ploidy=8)
+testdata <- read.Structure(myfile, ploidy=8)
 
 # examine the results
 testdata

man/read.Tetrasat.Rd

@@ -64,14 +64,8 @@ Lindsay V. Clark
 \code{\link{read.STRand}}
 }
 \examples{
-\dontrun{
-# example from the Tetrasat website
-mydata <- read.Tetrasat("http://markwith.freehomepage.com/sample.txt")
-summary(mydata)
-viewGenotypes(mydata, loci="A1_Gtype")
-}
-
 # example with defined data:
+myfile <- tempfile()
 cat("Sample Data", "A1_Gtype", "A10_Gtype", "B1_Gtype", "D7_Gtype",
 "D9_Gtype", "D12_Gtype", "Pop",
 "BCRHE 1             0406     04040404 0208     02020202 03030303 0710",
@@ -95,8 +89,8 @@ cat("Sample Data", "A1_Gtype", "A10_Gtype", "B1_Gtype", "D7_Gtype",
 "BR 7                0304     04040404 0809     02020202 03030303 070910",
 "BR 8                030406   04040404 07070707 02020202 03030303 070910",
 "BR 9                0406     04040404 07070707 02020202 03030303 07070707",
-sep="\n", file="TetrasatExample.txt")
-mydata2 <- read.Tetrasat("TetrasatExample.txt")
+sep="\n", file=myfile)
+mydata2 <- read.Tetrasat(myfile)
 
 summary(mydata2)
 viewGenotypes(mydata2, loci="B1_Gtype")

man/write.ATetra.Rd

@@ -73,11 +73,16 @@ PopNames(mygendata) <- c("this pop", "that pop")
 Ploidies(mygendata) <- 4
 Description(mygendata) <- "Example for write.ATetra."
 
+\dontrun{
 # write an ATetra file
 write.ATetra(mygendata, file="atetratest.txt")
 
 # view the file
 cat(readLines("atetratest.txt"),sep="\n")
+}
+\dontshow{
+write.ATetra(mygendata, file=tempfile())
+}
 
 }
 \keyword{ file }

man/write.GeneMapper.Rd

@@ -93,10 +93,15 @@ Genotypes(mygendata, loci="loc2") <- list(c(78,81,84),
                                           c(87), c(-9))
 Ploidies(mygendata) <- 6
 
+\dontrun{
 # write a GeneMapper file
 write.GeneMapper(mygendata, "exampleGMoutput.txt")
 
 # view the file with read.table
 read.table("exampleGMoutput.txt", sep="\t", header=TRUE)
 }
+\dontshow{
+write.GeneMapper(mygendata, tempfile())
+}
+}
 \keyword{ file }

man/write.GenoDive.Rd

@@ -95,8 +95,14 @@ PopInfo(mygendata) <- c(2,1,2,1,1,2,2,2,1)
 Ploidies(mygendata) <- c(2,2,2,2,2,2,2,3,2)
 Description(mygendata) <- "Serenity crew"
 
+\dontrun{
 # write files (use file="" to write to the console instead)
 write.GenoDive(mygendata, digits=2, file="testGenoDive2.txt")
 write.GenoDive(mygendata, digits=3, file="testGenoDive3.txt")
 }
+\dontshow{
+write.GenoDive(mygendata, digits=2, file=tempfile())
+write.GenoDive(mygendata, digits=3, file=tempfile())
+}
+}
 \keyword{file}

man/write.POPDIST.Rd

@@ -91,11 +91,16 @@ Genotypes(mygen, loci="loc1") <- list(c(128, 134), c(130),
 Genotypes(mygen, loci="loc27") <- list(c(209,211), c(207,217),
                                        c(207,209,215,221), c(211,223))
 
+\dontrun{
 # write the file
 write.POPDIST(mygen, file="forPOPDIST.txt")
 
 # view the file
 cat(readLines("forPOPDIST.txt"), sep="\n")
+}
+\dontshow{
+write.POPDIST(mygen, file=tempfile())
+}
 
 }
 \keyword{ file }

man/write.SPAGeDi.Rd

@@ -117,9 +117,15 @@ PopInfo(mygendata) <- c(1,1,2,2)
 myspatcoord <- data.frame(X=c(27,29,24,30), Y=c(44,41,45,46),
                           row.names=c("ind1","ind2","ind3","ind4"))
 
+\dontrun{
 # write a file
 write.SPAGeDi(mygendata, spatcoord = myspatcoord,
               file="SpagOutExample.txt")
 }
+\dontshow{
+write.SPAGeDi(mygendata, spatcoord = myspatcoord,
+              file=tempfile())
+}
+}
 \keyword{ file }
 

man/write.Tetrasat.Rd

@@ -91,10 +91,15 @@ PopInfo(mygendata) <- c(1,2,1,2)
 Description(mygendata) <- "An example for write.Tetrasat."
 Ploidies(mygendata) <- 4
 
+\dontrun{
 # write a Tetrasat file
 write.Tetrasat(mygendata, file="tetrasattest.txt")
 
 # view the file
 cat(readLines("tetrasattest.txt"),sep="\n")
 }
+\dontshow{
+write.Tetrasat(mygendata, file=tempfile())
+}
+}
 \keyword{file}

man/write.freq.SPAGeDi.Rd

@@ -148,7 +148,7 @@ myfreq2 <- data.frame(row.names=c("G","R"), Genomes=c(120,200),
              abc.134=c(0.53, 0.3))
 myusatnts <- as.integer(2)
 names(myusatnts) <- "abc"
-write.freq.SPAGeDi(myfreq2, usatnts=myusatnts, file="SPAGfreqExample2.txt")
+write.freq.SPAGeDi(myfreq2, usatnts=myusatnts, file=tempfile())
 }
 
 }