Still passing with _R_CHECK_LENGTH_1_LOGIC2_=FALSE, still failling wi…

…th _R_CHECK_LENGTH_1_LOGIC2_=TRUE
sneumann · Feb 10, 2020 · 34795a2 · 34795a2
1 parent 9e95680
commit 34795a2
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Showing 3 changed files with 20 additions and 9 deletions.
diff --git a/R/fct_findIsotopes.R b/R/fct_findIsotopes.R
@@ -55,6 +55,8 @@ findIsotopesPspec <- function(isomatrix, mz, ipeak, int, params){
         }
 
         ## IM - isotope matrix (column diffs(min,max) per charge, row num. isotope)
+        ## STN: isn't it rather:
+        ## IM - isotope matrix (column diffs(min,max) per ISOTOPE, row num. charge state)
         IM <- t(sapply(1:params$maxcharge,function(x){
             mzmin <- (params$IM[, "mzmin"]) / x;
             mzmax <- (params$IM[, "mzmax"]) / x;
@@ -85,11 +87,20 @@ findIsotopesPspec <- function(isomatrix, mz, ipeak, int, params){
         for(iso in 1:min(params$maxiso,ncol(hits.iso))){
             hit <- apply(hits.iso,1, function(x) any(CAMERA:::naOmit(x)==iso))
             hit[which(is.na(hit))] <- TRUE
-            if(all(hit)) break;
+            if(all(hit))
+                break;
             hits.iso[!hit,] <- t(apply(hits.iso[!hit,,drop=FALSE],1, function(x) {
                 if(!all(is.na(x))){
                     ini <- which(x > iso)
-                    if(!is.infinite(ini) && length(ini) > 0){
+
+                    ## Here the following condition was previously:
+                    ## if(!is.infinite(ini) && length(ini) > 0){
+                    ##
+                    ## The fix for issue #44 assumes the follwoing:
+                    ## "There is at least one hit" Not sure why
+                    ## ini as return value of which() would contain inf at all
+
+                    if(!is.infinite(ini)[1] & length(ini) > 0){
                         x[min(ini):ncol(hits.iso)] <- NA  
                     }
                 }
@@ -213,8 +224,8 @@ findIsotopesPspec <- function(isomatrix, mz, ipeak, int, params){
                     break;
                 }
             }
-        }#end for charge
-    }#end for j
+        }# for(charge in 1:nrow(candidate.matrix)){
+    }# end for ( j in 1:(length(mz) - 1)){
 
     return(isomatrix)
 }

diff --git a/R/pspec2metfrag.R b/R/pspec2metfrag.R
@@ -15,7 +15,7 @@ extractfragments <- function(object, pspecidx=NULL) {
     sp <- getpspectra(object, grp=pspec)
     rt <- median(sp[, "rt"])
     peakID <- object@pspectra[[pspec]]
-    if(object@sample == 1 && length(sampnames(object@xcmsSet)) == 1){
+    if(object@sample == 1 & length(sampnames(object@xcmsSet)) == 1){
         #single sample
         #intIdx <- intVal;
         intIdx <- "maxo";

diff --git a/R/xsAnnotate.R b/R/xsAnnotate.R
@@ -9,7 +9,7 @@ xsAnnotate <- function(xs=NULL, sample=NA, nSlaves=1, polarity=NULL){
 
   object  <- new("xsAnnotate");
 
-  if(length(sampnames(xs)) > 1 && !nrow(xs@groups) > 0) {  
+  if(length(sampnames(xs)) > 1 & !nrow(xs@groups) > 0) {  
       # more than one sample
       # checking alignment
       stop ('First argument must be a xcmsSet with group information or contain only one sample.') 
@@ -19,7 +19,7 @@ xsAnnotate <- function(xs=NULL, sample=NA, nSlaves=1, polarity=NULL){
   if(length(sample) > 1){
     #example sample <- c(1,2,3,4,5)
 
-    if(all(sample < length(xs@filepaths) && sample > 0)){
+    if(all(sample <= length(xs@filepaths)) & all(sample > 0)){
       #all sample values are in allowed range
       object@sample <- sample;
     }else{
@@ -785,7 +785,7 @@ setMethod("findAdducts", "xsAnnotate", function(object, ppm=5, mzabs=0.015, mult
     object@pspectra[[1]] <- seq(1:nrow(object@groupInfo)); 
   }
 
-  if(object@sample == 1 && length(sampnames(object@xcmsSet)) == 1){
+  if(object@sample == 1 & length(sampnames(object@xcmsSet)) == 1){
     ##one sample case
     mint <- object@groupInfo[, intval];
   }else{
@@ -1266,7 +1266,7 @@ setMethod("getPeaklist", "xsAnnotate", function(object, intval="into") {
 
   #generate peaktable
   #Check if xcmsSet contains only one sample
-  if(object@sample == 1 && length(sampnames(object@xcmsSet)) == 1){
+  if(object@sample == 1 & length(sampnames(object@xcmsSet)) == 1){
     #intval is here ignored since all intensity values are already contained
     peaktable <- object@groupInfo;
   }else {