Updated vignettes for 0.22 release

man/NMF-package.Rd

@@ -15,8 +15,8 @@ parallel computations on multicore machines.
   \tabular{ll}{
 Package: \tab NMF\cr
 Type: \tab Package\cr
-Version: \tab 0.21.3\cr
-Date: \tab 2013-09-17\cr
+Version: \tab 0.22\cr
+Date: \tab 2014-12-04\cr
 License: \tab GPL (>=2)\cr
 LazyLoad: \tab yes\cr
 }

vignettes/NMF-unitTests.Rnw

@@ -17,15 +17,15 @@ authors <- packageDescription(pkg)$Author
 
 \usepackage[colorlinks]{hyperref}
 \author{\Sexpr{authors}}
-\title{\texttt{\Sexpr{pkg}}: Unit testing results\footnote{Vignette computed  on Fri Sep 12 15:05:04 2014}}
+\title{\texttt{\Sexpr{pkg}}: Unit testing results\footnote{Vignette computed  on Thu Dec  4 14:44:18 2014}}
 \date{\texttt{\Sexpr{pkg}} version \Sexpr{prettyVersion} as of \Sexpr{prettyDate}}
 \begin{document}
 \maketitle
 
 \section{Details}
 \begin{verbatim}
 
-RUNIT TEST PROTOCOL -- Fri Sep 12 15:05:04 2014 
+RUNIT TEST PROTOCOL -- Thu Dec  4 14:44:17 2014 
 *********************************************** 
 Number of test functions: 82 
 Number of deactivated test functions: 4 
@@ -44,146 +44,146 @@ Test Suite: package:NMF
 Test function regexp: ^test. 
 Test file regexp: ^runit.*.[rR]$ 
 Involved directory: 
-/tmp/Rpkglib_2c36516f9490/NMF/tests 
+/tmp/Rpkglib_21df4678e6e5/NMF/tests 
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.aheatmap.R 
-test.mfrow: (1 checks) ... OK (0.62 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.aheatmap.R 
+test.mfrow: (1 checks) ... OK (0.49 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.algorithms.r 
-test.brunet: (16 checks) ... OK (4.98 seconds)
-test.cversions.brunet: (1 checks) ... OK (1.21 seconds)
-test.cversions.lee: (1 checks) ... OK (1.14 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.algorithms.r 
+test.brunet: (16 checks) ... OK (3.6 seconds)
+test.cversions.brunet: (1 checks) ... OK (0.89 seconds)
+test.cversions.lee: (1 checks) ... OK (1.09 seconds)
 test.cversions.lnmf : DEACTIVATED, Algorithm 'lnmf' is not fully working.
-test.cversions.ns: (1 checks) ... OK (1.15 seconds)
-test.cversions.offset: (1 checks) ... OK (2.63 seconds)
-test.frobenius: (16 checks) ... OK (7.78 seconds)
-test.KL: (16 checks) ... OK (6.28 seconds)
-test.lee: (16 checks) ... OK (3.72 seconds)
+test.cversions.ns: (1 checks) ... OK (1.18 seconds)
+test.cversions.offset: (1 checks) ... OK (2.01 seconds)
+test.frobenius: (16 checks) ... OK (5.06 seconds)
+test.KL: (16 checks) ... OK (4.41 seconds)
+test.lee: (16 checks) ... OK (4.72 seconds)
 test.lnmf : DEACTIVATED, Algorithm 'lnmf' is not fully working.
-test.ns: (16 checks) ... OK (7 seconds)
-test.offset: (16 checks) ... OK (10.53 seconds)
-test.port_brunet: (9 checks) ... OK (4.29 seconds)
-test.snmf: (44 checks) ... OK (11.67 seconds)
+test.ns: (16 checks) ... OK (4.52 seconds)
+test.offset: (16 checks) ... OK (5.07 seconds)
+test.port_brunet: (9 checks) ... OK (12.86 seconds)
+test.snmf: (44 checks) ... OK (9.92 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.bioc.r 
-test.access: (26 checks) ... OK (0.06 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.bioc.r 
+test.access: (26 checks) ... OK (0.03 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.distance.r 
-test.KL: (9 checks) ... OK (2.6 seconds)
-test.rss: (4 checks) ... OK (0.08 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.distance.r 
+test.KL: (9 checks) ... OK (1.8 seconds)
+test.rss: (4 checks) ... OK (0.17 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.interface.r 
-test.compare: (5 checks) ... OK (14.77 seconds)
-test.nmf.callback: (22 checks) ... OK (28.84 seconds)
-test.nmf.custom: (87 checks) ... OK (1.68 seconds)
-test.nmf.default: (8 checks) ... OK (0.26 seconds)
-test.nmf.dots: (11 checks) ... OK (0.86 seconds)
-test.nmf.method: (36 checks) ... OK (12.33 seconds)
-test.nmf.model: (22 checks) ... OK (0.74 seconds)
-test.nmfModel.formula: (12 checks) ... OK (1.06 seconds)
-test.nmf.multirank: (10 checks) ... OK (9.26 seconds)
-test.nmf.options: (18 checks) ... OK (11.36 seconds)
-test.nmf.parameters: (53 checks) ... OK (1.03 seconds)
-test.nmf.seed.argument: (149 checks) ... OK (14.19 seconds)
-test.nmf.seed.equivalent: (11 checks) ... OK (20.81 seconds)
-test.nmf.seed.fault: (4 checks) ... OK (4.35 seconds)
-test.nmf.seed.repro: (8 checks) ... OK (18.56 seconds)
-test.nmf.stop: (6 checks) ... OK (1.84 seconds)
-test.parallel: (6 checks) ... OK (14.73 seconds)
-test.registry: (9 checks) ... OK (0.41 seconds)
-test.seed: (33 checks) ... OK (0.48 seconds)
-test.summary: (3 checks) ... OK (5.03 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.interface.r 
+test.compare: (5 checks) ... OK (15.96 seconds)
+test.nmf.callback: (22 checks) ... OK (24.52 seconds)
+test.nmf.custom: (87 checks) ... OK (2.27 seconds)
+test.nmf.default: (8 checks) ... OK (0.35 seconds)
+test.nmf.dots: (11 checks) ... OK (1.06 seconds)
+test.nmf.method: (36 checks) ... OK (18.33 seconds)
+test.nmf.model: (22 checks) ... OK (0.98 seconds)
+test.nmfModel.formula: (12 checks) ... OK (2.39 seconds)
+test.nmf.multirank: (10 checks) ... OK (8.43 seconds)
+test.nmf.options: (18 checks) ... OK (7.69 seconds)
+test.nmf.parameters: (53 checks) ... OK (1.96 seconds)
+test.nmf.seed.argument: (149 checks) ... OK (15.18 seconds)
+test.nmf.seed.equivalent: (11 checks) ... OK (15.87 seconds)
+test.nmf.seed.fault: (4 checks) ... OK (3.68 seconds)
+test.nmf.seed.repro: (8 checks) ... OK (17.07 seconds)
+test.nmf.stop: (6 checks) ... OK (2.33 seconds)
+test.parallel: (6 checks) ... OK (16.13 seconds)
+test.registry: (9 checks) ... OK (0.5 seconds)
+test.seed: (33 checks) ... OK (0.29 seconds)
+test.summary: (3 checks) ... OK (4.11 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.NMFclass.r 
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.NMFclass.r 
 test.basis: (2 checks) ... OK (0.01 seconds)
-test.class.NMFns: (65 checks) ... OK (0.19 seconds)
-test.class.NMFstd: (28 checks) ... OK (0.01 seconds)
-test.coef: (2 checks) ... OK (0 seconds)
-test.connectivity: (3 checks) ... OK (0.01 seconds)
-test.deviance: (9 checks) ... OK (0.01 seconds)
+test.class.NMFns: (65 checks) ... OK (0.07 seconds)
+test.class.NMFstd: (28 checks) ... OK (0.02 seconds)
+test.coef: (2 checks) ... OK (0.01 seconds)
+test.connectivity: (3 checks) ... OK (0.02 seconds)
+test.deviance: (9 checks) ... OK (0.04 seconds)
 test.dimensions: (4 checks) ... OK (0 seconds)
-test.dimnames: (173 checks) ... OK (0.07 seconds)
-test.entropy: (5 checks) ... OK (0 seconds)
-test.misc: (9 checks) ... OK (0 seconds)
-test.nmfModel: (363 checks) ... OK (0.11 seconds)
-test.NMF.rnmf: (93 checks) ... OK (1.2 seconds)
+test.dimnames: (173 checks) ... OK (0.17 seconds)
+test.entropy: (5 checks) ... OK (0.01 seconds)
+test.misc: (9 checks) ... OK (0.01 seconds)
+test.nmfModel: (363 checks) ... OK (0.27 seconds)
+test.NMF.rnmf: (93 checks) ... OK (1.84 seconds)
 test.predict: (10 checks) ... OK (0.01 seconds)
 test.purity: (5 checks) ... OK (0 seconds)
 test.sparseness: (13 checks) ... OK (0.01 seconds)
-test.subset: (50 checks) ... OK (0.04 seconds)
-test.syntheticNMF: (5 checks) ... OK (1.26 seconds)
+test.subset: (50 checks) ... OK (0.07 seconds)
+test.syntheticNMF: (5 checks) ... OK (1.53 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.NMFfit-class.r 
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.NMFfit-class.r 
 test.deviance: (0 checks) ... OK (0 seconds)
-test.isNMFfit: (6 checks) ... OK (4.26 seconds)
-test.niter: (4 checks) ... OK (1.76 seconds)
-test.nmf.equal: (304 checks) ... OK (1.99 seconds)
+test.isNMFfit: (6 checks) ... OK (3.44 seconds)
+test.niter: (4 checks) ... OK (1.84 seconds)
+test.nmf.equal: (304 checks) ... OK (4.48 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.NMFSet.r 
-test.fit: (9 checks) ... OK (6.17 seconds)
-test.interface: (6 checks) ... OK (2.16 seconds)
-test.join.multipleAndSingleRunsMethods: (2 checks) ... OK (6.78 seconds)
-test.join.multipleRuns: (2 checks) ... OK (7.14 seconds)
-test.join.singleRuns: (7 checks) ... OK (2.34 seconds)
-test.multipleruns: (2 checks) ... OK (2.27 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.NMFSet.r 
+test.fit: (9 checks) ... OK (4.69 seconds)
+test.interface: (6 checks) ... OK (2.76 seconds)
+test.join.multipleAndSingleRunsMethods: (2 checks) ... OK (5.55 seconds)
+test.join.multipleRuns: (2 checks) ... OK (6.31 seconds)
+test.join.singleRuns: (7 checks) ... OK (0.79 seconds)
+test.multipleruns: (2 checks) ... OK (2.25 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.NMFStrategy-class.r 
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.NMFStrategy-class.r 
 test.accessors: (26 checks) ... OK (0.04 seconds)
-test.constructor: (16 checks) ... OK (0.04 seconds)
-test.constructorMethod: (3 checks) ... OK (0.02 seconds)
+test.constructor: (16 checks) ... OK (0.05 seconds)
+test.constructorMethod: (3 checks) ... OK (0.03 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.options.r 
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.options.r 
 test.nmf.getOption: (2 checks) ... OK (0 seconds)
-test.nmf.options: (9 checks) ... OK (0 seconds)
+test.nmf.options: (9 checks) ... OK (0.01 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.parallel.r 
-test.ForeachBackend: (4 checks) ... OK (3.1 seconds)
-test.gVariable: (11 checks) ... OK (21.18 seconds)
-test.nmf: (59 checks) ... OK (94.31 seconds)
-test.setupBackend: (4 checks) ... OK (0.12 seconds)
-test.shared_memory_doMC: (12 checks) ... OK (6.22 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.parallel.r 
+test.ForeachBackend: (4 checks) ... OK (3.17 seconds)
+test.gVariable: (11 checks) ... OK (18.51 seconds)
+test.nmf: (59 checks) ... OK (75.32 seconds)
+test.setupBackend: (4 checks) ... OK (0.13 seconds)
+test.shared_memory_doMC: (12 checks) ... OK (6.13 seconds)
 test.shared_memory_doMPI : DEACTIVATED, NMF shared memory feature does not currently work with doMPI.
-test.shared_memory_doParallel: (12 checks) ... OK (11.97 seconds)
-test.shared_memory_doSEQ: (11 checks) ... OK (6.55 seconds)
+test.shared_memory_doParallel: (12 checks) ... OK (10 seconds)
+test.shared_memory_doSEQ: (11 checks) ... OK (6.52 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.seed.r 
-test.nndsvd: (10 checks) ... OK (0.04 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.seed.r 
+test.nndsvd: (10 checks) ... OK (0.02 seconds)
 test.none: (6 checks) ... OK (0.03 seconds)
-test.random: (26 checks) ... OK (0.13 seconds)
+test.random: (26 checks) ... OK (0.12 seconds)
 test.restore : DEACTIVATED, The option 'restore.seed' is deprecated. Related tests are now in test.seed.effect
-test.seed.effect: (15 checks) ... OK (20.84 seconds)
-test.zzz.all: (297 checks) ... OK (18.04 seconds)
+test.seed.effect: (15 checks) ... OK (18.58 seconds)
+test.zzz.all: (297 checks) ... OK (18.13 seconds)
 --------------------------- 
-Test file: /tmp/Rpkglib_2c36516f9490/NMF/tests/runit.utils.r 
-test.nmfWrapper: (16 checks) ... OK (0.98 seconds)
-test.rmatrix: (16 checks) ... OK (0.02 seconds)
+Test file: /tmp/Rpkglib_21df4678e6e5/NMF/tests/runit.utils.r 
+test.nmfWrapper: (16 checks) ... OK (2.14 seconds)
+test.rmatrix: (16 checks) ... OK (0.04 seconds)
 
 Total execution time
 ***************************
    user  system elapsed 
-412.399  44.494 462.030 
+389.370  37.686 424.702 
 
 \end{verbatim}
 
 \section*{Session Information}
 \begin{itemize}\raggedright
-  \item R version 3.1.1 (2014-07-10), \verb|x86_64-pc-linux-gnu|
+  \item R version 3.1.2 (2014-10-31), \verb|x86_64-pc-linux-gnu|
   \item Locale: \verb|LC_CTYPE=en_US.UTF-8|, \verb|LC_NUMERIC=C|, \verb|LC_TIME=C|, \verb|LC_COLLATE=en_US.UTF-8|, \verb|LC_MONETARY=en_ZA.UTF-8|, \verb|LC_MESSAGES=en_US.UTF-8|, \verb|LC_PAPER=en_ZA.UTF-8|, \verb|LC_NAME=C|, \verb|LC_ADDRESS=C|, \verb|LC_TELEPHONE=C|, \verb|LC_MEASUREMENT=en_ZA.UTF-8|, \verb|LC_IDENTIFICATION=C|
   \item Base packages: base, datasets, graphics, grDevices, methods,
     parallel, stats, utils
-  \item Other packages: BH~1.54.0-3, bigmemory~4.4.6,
-    bigmemory.sri~0.1.3, Biobase~2.24.0, BiocGenerics~0.10.0,
-    cluster~1.15.2, doMPI~0.2, doParallel~1.0.8, fastICA~1.2-0,
-    foreach~1.4.2, iterators~1.0.7, NMF~0.21.3, pkgmaker~0.25.7,
-    RColorBrewer~1.0-5, Rcpp~0.11.2, RcppOctave~0.14.1, registry~0.2,
-    Rmpi~0.6-5, rngtools~1.2.4, RUnit~0.4.26, stringr~0.6.2,
+  \item Other packages: BH~1.54.0-5, bigmemory~4.4.6,
+    bigmemory.sri~0.1.3, Biobase~2.26.0, BiocGenerics~0.12.1,
+    cluster~1.15.3, doMPI~0.2, doParallel~1.0.8, fastICA~1.2-0,
+    foreach~1.4.2, iterators~1.0.7, NMF~0.22, pkgmaker~0.25.9,
+    RColorBrewer~1.0-5, Rcpp~0.11.3, RcppOctave~0.14.5, registry~0.2,
+    Rmpi~0.6-5, rngtools~1.2.4, RUnit~0.4.27, stringr~0.6.2,
     synchronicity~1.1.4
   \item Loaded via a namespace (and not attached): codetools~0.2-9,
-    colorspace~1.2-4, compiler~3.1.1, dendextend~0.17.1, digest~0.6.4,
-    ggplot2~1.0.0, grid~3.1.1, gridBase~0.4-7, gtable~0.1.2,
-    magrittr~1.0.1, MASS~7.3-34, munsell~0.4.2, plyr~1.8.1,
-    proto~0.3-10, reshape2~1.4, scales~0.2.4, tools~3.1.1,
-    whisker~0.3-2, xtable~1.7-3
+    colorspace~1.2-4, compiler~3.1.2, dendextend~0.17.5, digest~0.6.4,
+    ggplot2~1.0.0, grid~3.1.2, gridBase~0.4-7, gtable~0.1.2,
+    magrittr~1.5, MASS~7.3-35, munsell~0.4.2, plyr~1.8.1, proto~0.3-10,
+    reshape2~1.4, scales~0.2.4, tools~3.1.2, whisker~0.3-2,
+    xtable~1.7-4
 \end{itemize}
 
 \end{document}