version 1.8-22

TristansCloud · Sep 18, 2017 · b1e2933 · b1e2933
1 parent 0c52529
commit b1e2933
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: mgcv
-Version: 1.8-21
+Version: 1.8-22
 Author: Simon Wood <simon.wood@r-project.org>
 Maintainer: Simon Wood <simon.wood@r-project.org>
 Title: Mixed GAM Computation Vehicle with Automatic Smoothness
@@ -18,6 +18,6 @@ LazyLoad: yes
 ByteCompile: yes
 License: GPL (>= 2)
 NeedsCompilation: yes
-Packaged: 2017-09-15 08:10:23 UTC; sw283
+Packaged: 2017-09-18 10:38:41 UTC; sw283
 Repository: CRAN
-Date/Publication: 2017-09-17 19:24:02 UTC
+Date/Publication: 2017-09-24 15:24:05 UTC
diff --git a/MD5 b/MD5
@@ -1,8 +1,8 @@
-d2e550a4fc7d0141a6ba96400cc76ab8 *ChangeLog
-cecd2e1e20565bb275902be2ece15b62 *DESCRIPTION
+bc8bc8be9cec065f0c7ec0cf670516f2 *ChangeLog
+61563afa209f2b618f33097136c35bb2 *DESCRIPTION
 eb723b61539feef013de476e68b5c50a *GPL-2
 9fa89dc9361930dca536d4e011e4e605 *NAMESPACE
-eaf241e6d0bd26d3f4031988884a47a4 *R/bam.r
+b051474f30e8e779f2440e8ecd5bbd51 *R/bam.r
 7b419683b0948cf6da009f614078fe90 *R/coxph.r
 777a0d67a1f7fa14bf87bc312064061b *R/efam.r
 dfdb821247da3e780de0d4599b88735d *R/fast-REML.r
@@ -42,7 +42,7 @@ fd0cfd64be579f9fbecdbb7f2b8ec1eb *man/Sl.initial.repara.Rd
 60670020425f8749b81a8d8c3f168880 *man/Sl.setup.Rd
 69ae63833438a3af2963e39482f1d72f *man/Tweedie.Rd
 8087ab00d10b44c99c37f49bf90e19cd *man/anova.gam.Rd
-a7e0ce83164f1e34d0a9d99d0f9853f3 *man/bam.Rd
+6180a4e9ea206e1a350b993dade0a869 *man/bam.Rd
 ab5e37c3bf8803de63b63c3bdc5909cd *man/bam.update.Rd
 cf5f1ee0aab639c7c4b9b357434f15b2 *man/bandchol.Rd
 745cbf31eb14fc1c5916fc634c74d998 *man/bug.reports.mgcv.Rd

diff --git a/R/bam.r b/R/bam.r
@@ -1855,7 +1855,7 @@ AR.resid <- function(rsd,rho=0,AR.start=NULL) {
 bam <- function(formula,family=gaussian(),data=list(),weights=NULL,subset=NULL,na.action=na.omit,
                 offset=NULL,method="fREML",control=list(),select=FALSE,scale=0,gamma=1,knots=NULL,sp=NULL,
                 min.sp=NULL,paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discrete=FALSE,
-                cluster=NULL,nthreads=NA,gc.level=1,use.chol=FALSE,samfrac=1,coef=NULL,
+                cluster=NULL,nthreads=1,gc.level=1,use.chol=FALSE,samfrac=1,coef=NULL,
                 drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.intercept=NULL,...)
 
 ## Routine to fit an additive model to a large dataset. The model is stated in the formula, 
@@ -1894,7 +1894,7 @@ bam <- function(formula,family=gaussian(),data=list(),weights=NULL,subset=NULL,n
         warning("discretization only available with fREML")
       } else {
         if (!is.null(cluster)) warning("discrete method does not use parallel cluster - use nthreads instead")
-	if (nthreads>1 && !mgcv.omp()) warning("openMP not available: single threaded computation only")
+	if (is.finite(nthreads) && nthreads>1 && !mgcv.omp()) warning("openMP not available: single threaded computation only")
       }
     }  
     if (inherits(family,"extended.family")) {

diff --git a/changeLog b/changeLog
@@ -4,6 +4,11 @@
 Currently deprecated and liable to be removed:
 - gam performance iteration (1.8-19, Sept 2017)
 
+1.8-22
+
+* Fix of bug whereby testing for OpenMP and nthreads>1 in bam, would fail if 
+  OpenMP was missing. 
+
 1.8-21
 
 * When functions were added to families within mgcv some very large 

diff --git a/man/bam.Rd b/man/bam.Rd
@@ -21,7 +21,7 @@ bam(formula,family=gaussian(),data=list(),weights=NULL,subset=NULL,
     na.action=na.omit, offset=NULL,method="fREML",control=list(),
     select=FALSE,scale=0,gamma=1,knots=NULL,sp=NULL,min.sp=NULL,
     paraPen=NULL,chunk.size=10000,rho=0,AR.start=NULL,discrete=FALSE,
-    cluster=NULL,nthreads=NA,gc.level=1,use.chol=FALSE,samfrac=1,
+    cluster=NULL,nthreads=1,gc.level=1,use.chol=FALSE,samfrac=1,
     coef=NULL,drop.unused.levels=TRUE,G=NULL,fit=TRUE,drop.intercept=NULL,...)
 }
 %- maybe also `usage' for other objects documented here.
@@ -135,7 +135,7 @@ single machine). See details and example code.
 }
 
 \item{nthreads}{Number of threads to use for non-cluster computation (e.g. combining results from cluster nodes).
-if \code{NA} set to \code{max(1,length(cluster))}.}
+If \code{NA} set to \code{max(1,length(cluster))}.}
 
 \item{gc.level}{to keep the memory footprint down, it helps to call the garbage collector often, but this takes 
 a substatial amount of time. Setting this to zero means that garbage collection only happens when R decides it should. Setting to 2 gives frequent garbage collection. 1 is in between.}