1. mzR
  2. inst
  3. unitTests
  4. test_isolationWindow.R
Browse code

Remove Ramp backend with dependencies

jorainer authored on 20/09/2021 12:19:56
Showing 1 changed files
inst/unitTests/test_isolationWindow.R
History View file @ e3f79ff5f7
... ... 
@@ -2,21 +2,16 @@ test_isolationWindow <- function() {
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     library("msdata")
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     f <- msdata::proteomics(full.names = TRUE,
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                             pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
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-    rw1 <- openMSfile(f, backend = "Ramp")
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     rw2 <- openMSfile(f, backend = "pwiz")
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     i1 <- isolationWindow(f)
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-    i2 <- isolationWindow(rw1)
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     i3 <- isolationWindow(rw2)
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-    checkEquals(i1, i2)
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     checkEquals(i1, i3)
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     i1 <- isolationWindow(f, unique = FALSE)
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-    i2 <- isolationWindow(rw1, unique = FALSE)
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     i3 <- isolationWindow(rw2, unique = FALSE)
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-    checkEquals(i1, i2)
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     checkEquals(i1, i3)
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     i1 <- isolationWindow(c(f, f), unique = FALSE)
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     checkEquals(length(i1), 2L)
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     checkEquals(i1[[1]], i1[[2]])
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-    hd <- header(rw1)
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+    hd <- header(rw2)
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     checkEquals(sum(hd$msLevel == 2), nrow(i1[[1]]))
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 }
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specify full name as pattern for get the small TMT Erwinia subset

Laurent authored on 23/06/2017 15:24:36
Showing 1 changed files
inst/unitTests/test_isolationWindow.R
History View file @ d05a987e4e
... ... 
@@ -1,6 +1,7 @@
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 test_isolationWindow <- function() {
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     library("msdata")
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-    f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_")
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+    f <- msdata::proteomics(full.names = TRUE,
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+                            pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
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     rw1 <- openMSfile(f, backend = "Ramp")
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     rw2 <- openMSfile(f, backend = "pwiz")
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     i1 <- isolationWindow(f)
Browse code

Merge branch 'master' into devel

* master:
Fix failing example and test due to updated msdata::protemics data

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@122002 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 06/10/2016 22:09:03
Showing 1 changed files
inst/unitTests/test_isolationWindow.R
History View file @ d0a950cbc2
... ... 
@@ -1,6 +1,6 @@
1 1 
 test_isolationWindow <- function() {
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     library("msdata")
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-    f <- msdata::proteomics(full.names = TRUE)
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+    f <- msdata::proteomics(full.names = TRUE, pattern = "TMT_")
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     rw1 <- openMSfile(f, backend = "Ramp")
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     rw2 <- openMSfile(f, backend = "pwiz")
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     i1 <- isolationWindow(f)
Browse code

fix conflicts

From: Laurent <lg390@cam.ac.uk>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@121322 bc3139a8-67e5-0310-9ffc-ced21a209358

l.gatto authored on 23/09/2016 22:05:29
Showing 1 changed files
inst/unitTests/test_isolationWindow.R
History View file @ fdd95c087f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,21 @@
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+test_isolationWindow <- function() {
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+    library("msdata")
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+    f <- msdata::proteomics(full.names = TRUE)
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+    rw1 <- openMSfile(f, backend = "Ramp")
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+    rw2 <- openMSfile(f, backend = "pwiz")
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+    i1 <- isolationWindow(f)
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+    i2 <- isolationWindow(rw1)
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+    i3 <- isolationWindow(rw2)
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+    checkEquals(i1, i2)
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+    checkEquals(i1, i3)
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+    i1 <- isolationWindow(f, unique = FALSE)
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+    i2 <- isolationWindow(rw1, unique = FALSE)
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+    i3 <- isolationWindow(rw2, unique = FALSE)
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+    checkEquals(i1, i2)
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+    checkEquals(i1, i3)
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+    i1 <- isolationWindow(c(f, f), unique = FALSE)
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+    checkEquals(length(i1), 2L)
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+    checkEquals(i1[[1]], i1[[2]])
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+    hd <- header(rw1)
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+    checkEquals(sum(hd$msLevel == 2), nrow(i1[[1]]))
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+}