Browse code

Remove Test Find Primers & Version Bump

Juan Pablo Romero authored on 03/06/2019 16:31:35
Showing 4 changed files

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Binary files a/.DS_Store and b/.DS_Store differ
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@@ -2,7 +2,7 @@ Package: EventPointer
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 Type: Package
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 Title: An effective identification of alternative splicing events
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 	   using junction arrays and RNA-Seq data
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-Version: 2.3.3
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+Version: 2.3.4
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 Author: Juan Pablo Romero, Juan A. Ferrer-Bonsoms, Pablo Sacristan, Ander Muniategui, Fernando Carazo, Ander Aramburu, Angel Rubio
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 Maintainer: Juan Pablo Romero <jpromero@ceit.es>
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 Description: EventPointer is an R package to identify alternative splicing events 
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Binary files a/inst/.DS_Store and b/inst/.DS_Store differ
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deleted file mode 100644
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@@ -1,163 +0,0 @@
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-test_FindPrimers <- function() {
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-  
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-  obs <- tryCatch(FindPrimers(SG = NULL,
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-                EventNum = 4,
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-                Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE",
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-                Dir = "C:\\PROGRA~2\\primer3\\",
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-                taqman = 1,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10, 
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  
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-  checkIdentical("SG field is empty", obs)
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-  
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-  obs <- tryCatch(
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-    FindPrimers(SG = list(),
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-                EventNum = 0,
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-                Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE",
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-                Dir = "C:\\PROGRA~2\\primer3\\",
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-                taqman = 1,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10,
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  checkIdentical("EventNum field is empty or is not > 0", obs)
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-
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-  obs <- tryCatch(
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-    FindPrimers(SG = list(),
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-                EventNum = -45,
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-                Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE",
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-                Dir = "C:\\PROGRA~2\\primer3\\",
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-                taqman = 1,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10,
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  checkIdentical("EventNum field is empty or is not > 0", obs)
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-
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-  obs <- tryCatch(
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-    FindPrimers(SG = list(),
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-                EventNum = NULL,
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-                Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE",
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-                Dir = "C:\\PROGRA~2\\primer3\\",
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-                taqman = 1,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10,
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  checkIdentical("EventNum field is empty or is not > 0", obs)
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-  
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-  
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-  obs <- tryCatch(
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-    FindPrimers(SG = list(),
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-                EventNum = 4,
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-                Primer3Path = "",
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-                Dir = "C:\\PROGRA~2\\primer3\\",
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-                taqman = 1,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10,
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  checkIdentical("Primer3Path field should point to the .exe of Primers3.
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-         Check in the vignette for more information", obs)
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-  
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-  obs <- tryCatch(
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-    FindPrimers(SG = list(),
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-                EventNum = 4,
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-                Primer3Path = NULL,
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-                Dir = "C:\\PROGRA~2\\primer3\\",
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-                taqman = 1,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10,
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  checkIdentical("Primer3Path field is empty", obs)
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-  
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-  
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-  
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-  
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-  
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-  # obs <- tryCatch(
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-  #   FindPrimers(SG = list(),
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-  #               EventNum = 1,
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-  #               Primer3Path = "./inst/extdata/DONSON.gtf",
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-  #               Dir = "",
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-  #               taqman = 1,
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-  #               nProbes=1,
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-  #               nPrimerstwo=4,
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-  #               ncommonForward=4,
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-  #               ncommonReverse=4,
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-  #               nExons=10,
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-  #               nPrimers =5,
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-  #               maxLength = 1200), error=conditionMessage)
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-  # checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored", obs)
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-  # 
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-  
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-  
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-  obs <- tryCatch(
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-    FindPrimers(SG = list(),
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-                EventNum = 1,
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-                Primer3Path = "./inst/extdata/DONSON.gtf",
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-                Dir = NULL,
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-                taqman = 1,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10,
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  checkIdentical("Dir field is empty", obs)
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-  
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-  obs <- tryCatch(
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-    FindPrimers(SG = list(),
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-                EventNum = 1,
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-                Primer3Path = "./inst/extdata/DONSON.gtf",
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-                Dir = "C:\\PROGRA~2\\primer3\\",
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-                taqman = NA,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10,
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  checkIdentical("taqman field is empty", obs)
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-  
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-  
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-  obs <- tryCatch(
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-    FindPrimers(SG = list(),
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-                EventNum = 1,
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-                Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE",
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-                Dir = "C:\\PROGRA~2\\primer3\\",
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-                taqman = 3,
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-                nProbes=1,
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-                nPrimerstwo=4,
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-                ncommonForward=4,
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-                ncommonReverse=4,
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-                nExons=10,
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-                nPrimers =5,
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-                maxLength = 1200), error=conditionMessage)
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-  checkIdentical("taqman variable should be equal to 1 or 0", obs)
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-  
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-  
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-}