progress -- showing overall running time when completed

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SeqArray
 Type: Package
 Title: Big Data Management of Whole-genome Sequence Variant Calls
-Version: 1.15.6
-Date: 2017-04-10
+Version: 1.17.1
+Date: 2017-04-27
 Depends: R (>= 3.3.0), gdsfmt (>= 1.10.1)
 Imports: methods, parallel, S4Vectors, IRanges, GenomicRanges,
         GenomeInfoDb, SummarizedExperiment, Biostrings, VariantAnnotation

NEWS

@@ -1,5 +1,12 @@
+CHANGES IN VERSION 1.17.0-1.17.1
+
+    o progress information: showing overall running time when completed
+
+
 CHANGES IN VERSION 1.16.0
 
+-------------------------
+
     o a new argument 'intersect' in `seqSetFilter()` and `seqSetFilterChrom()`
 
     o a new function `seqSetFilterCond()`

src/Index.cpp

@@ -752,6 +752,27 @@ static const double S_HOUR =  60 * S_MIN;
 static const double S_DAY  =  24 * S_HOUR;
 static const double S_YEAR = 365 * S_DAY;
 
+static const char *time_str(double s)
+{
+	if (R_FINITE(s))
+	{
+		static char buffer[64];
+		if (s < S_MIN)
+			sprintf(buffer, "%.0fs", s);
+		else if (s < S_HOUR)
+			sprintf(buffer, "%.1fm", s/S_MIN);
+		else if (s < S_DAY)
+			sprintf(buffer, "%.1fh", s/S_HOUR);
+		else if (s < S_YEAR)
+			sprintf(buffer, "%.1fd", s/S_DAY);
+		else
+			sprintf(buffer, "%.1f years", s/S_YEAR);
+		return buffer;
+	} else
+		return "---";
+}
+
+
 CProgress::CProgress(C_Int64 start, C_Int64 count, SEXP conn, bool newline)
 {
 	TotalCount = count;
@@ -778,6 +799,7 @@ CProgress::CProgress(C_Int64 start, C_Int64 count, SEXP conn, bool newline)
 	}
 
 	time_t s; time(&s);
+	_start_time = s;
 	_timer.reserve(128);
 	_timer.push_back(pair<double, time_t>(percent, s));
 
@@ -837,37 +859,9 @@ void CProgress::ShowProgress()
 			// show
 			if (NewLine)
 			{
-				if (R_FINITE(s))
-				{
-					if (s < S_MIN)
-						ConnPutText(File, "[%s] %2.0f%%, ETC: %.0fs\n", bar, p, s);
-					else if (s < S_HOUR)
-						ConnPutText(File, "[%s] %2.0f%%, ETC: %.1fm\n", bar, p, s/S_MIN);
-					else if (s < S_DAY)
-						ConnPutText(File, "[%s] %2.0f%%, ETC: %.1fh\n", bar, p, s/S_HOUR);
-					else if (s < S_YEAR)
-						ConnPutText(File, "[%s] %2.0f%%, ETC: %.1fd\n", bar, p, s/S_DAY);
-					else
-						ConnPutText(File, "[%s] %2.0f%%, ETC: %.1f years\n", bar, p, s/S_YEAR);
-				} else {
-					ConnPutText(File, "[%s] %2.0f%%, ETC: ---\n", bar, p);
-				}
+				ConnPutText(File, "[%s] %2.0f%%, ETC: %s\n", bar, p, time_str(s));
 			} else {
-				if (R_FINITE(s))
-				{
-					if (s < S_MIN)
-						ConnPutText(File, "\r[%s] %2.0f%%, ETC: %.0fs  ", bar, p, s);
-					else if (s < S_HOUR)
-						ConnPutText(File, "\r[%s] %2.0f%%, ETC: %.1fm  ", bar, p, s/S_MIN);
-					else if (s < S_DAY)
-						ConnPutText(File, "\r[%s] %2.0f%%, ETC: %.1fh  ", bar, p, s/S_HOUR);
-					else if (s < S_YEAR)
-						ConnPutText(File, "\r[%s] %2.0f%%, ETC: %.1fd  ", bar, p, s/S_DAY);
-					else
-						ConnPutText(File, "\r[%s] %2.0f%%, ETC: %.1f years", bar, p, s/S_YEAR);
-				} else {
-					ConnPutText(File, "\r[%s] %2.0f%%, ETC: ---  ", bar, p);
-				}
+				ConnPutText(File, "\r[%s] %2.0f%%, ETC: %s  ", bar, p, time_str(s));
 				if (Counter >= TotalCount) ConnPutText(File, "\n");
 			}
 		} else {
@@ -931,27 +925,15 @@ void CProgressStdOut::ShowProgress()
 		p *= 100;
 
 		// show
+		_last_time = now;
 		if (Counter >= TotalCount)
 		{
-			Rprintf("\r[%s] 100%%, completed      \n", bar);
+			s = difftime(_last_time, _start_time);
+			Rprintf("\r[%s] 100%%, completed in %s\n", bar, time_str(s));
 		} else if ((interval >= 5) || (Counter <= 0))
 		{
 			_last_time = now;
-			if (R_FINITE(s))
-			{
-				if (s < S_MIN)
-					Rprintf("\r[%s] %2.0f%%, ETC: %.0fs  ", bar, p, s);
-				else if (s < S_HOUR)
-					Rprintf("\r[%s] %2.0f%%, ETC: %.1fm  ", bar, p, s/S_MIN);
-				else if (s < S_DAY)
-					Rprintf("\r[%s] %2.0f%%, ETC: %.1fh  ", bar, p, s/S_HOUR);
-				else if (s < S_YEAR)
-					Rprintf("\r[%s] %2.0f%%, ETC: %.1fd  ", bar, p, s/S_DAY);
-				else
-					Rprintf("\r[%s] %2.0f%%, ETC: %.1f years  ", bar, p, s/S_YEAR);
-			} else {
-				Rprintf("\r[%s] %2.0f%%, ETC: ---    ", bar, p);
-			}
+			Rprintf("\r[%s] %2.0f%%, ETC: %s    ", bar, p, time_str(s));
 		}
 	}
 }

src/Index.h

@@ -478,8 +478,9 @@ class COREARRAY_DLL_LOCAL CProgress
 
 protected:
 	C_Int64 TotalCount;  ///< the total number
-	C_Int64 Counter;  ///< the current counter
-	Rconnection File;  ///< R connection
+	C_Int64 Counter;     ///< the current counter
+	Rconnection File;    ///< R connection
+	time_t _start_time;  ///< the starting time
 	bool NewLine;
 	double _start, _step;
 	C_Int64 _hit;

vignettes/R_Integration.Rmd

@@ -136,7 +136,7 @@ Principal Component Analysis (PCA) is a common tool used in exploratory data ana
 # covariance variable with an initial value
 s <- 0
 
-seqApply(f, "$dosage", function(x)
+seqApply(file, "$dosage", function(x)
     {
         p <- 0.5 * mean(x, na.rm=TRUE)      # allele frequency
         g <- (x - 2*p) / sqrt(p*(1-p))      # normalized by allele frequency
@@ -153,9 +153,9 @@ eig <- eigen(s)
 
 ```
 [..................................................]  0%, ETC: --- 
-[=>................................................]  2%, ETC: 5.4m
+[==================>...............................] 36%, ETC: 4.1m
 ...
-[==================================================] 100%, completed
+[==================================================] 100%, completed in 14.3m
 ```
 
 ```R
@@ -180,7 +180,7 @@ eig <- eigen(s)
 [..................................................]  0%, ETC: ---
 [==================>...............................] 35%, ETC: 9s
 [======================================>...........] 75%, ETC: 3s
-[==================================================] 100%, completed
+[==================================================] 100%, completed in 14s
 ```
 
 `seqParallel()` utilizes the facilities offered by the R parallel package to perform calculations within a cluster or SMP environment, and the genotypes are automatically split into non-overlapping parts. The parallel implementation with R is shown as follows, and the C optimized function is also available in the SNPRelate package.
@@ -282,7 +282,7 @@ seqGDS2VCF(file, "exons.vcf.gz")
 ##     FORMAT Field: <none>
 ## 
 [..................................................]  0%, ETC: ---    
-[==================================================] 100%, completed      
+[==================================================] 100%, completed in 0s    
 ## Tue Jan  3 15:43:55 2017    Done.
 ```
 If random-access memory is sufficiently large, users could load all exon variants via `seqGetData(file, "genotype")`; otherwise, data have to be loaded by chunk or a user-defined function is applied over variants by `seqApply()`.