Browse code

clean up some warnings/errors from package check

sherman5 authored on 17/01/2018 18:57:26
Showing16 changed files

... ...
@@ -4,5 +4,22 @@
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 ^\.astylerc$
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 ^.*\.Rproj$
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 ^\.Rproj\.user$
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+
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 ^inst/benchmarks/
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-^inst/profiling/
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\ No newline at end of file
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+^inst/profiling/
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+^inst/vignettes/
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+
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+^src/Algorithms.o
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+^src/AtomicSupport.o
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+^src/Cogaps.o
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+^src/GibbsSampler.o
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+^src/Matrix.o
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+^src/Random.o
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+^src/RcppExports.o
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+^src/test-runner.o
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+^src/cpp_tests/testAlgorithms.o
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+^src/cpp_tests/testAtomicSupport.o
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+^src/cpp_tests/testGibbsSampler.o
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+^src/cpp_tests/testMatrix.o
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+^src/cpp_tests/testRandom.o
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+^src/cpp_tests/testSerialization.o
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\ No newline at end of file
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@@ -1,26 +1,10 @@
1 1
 # options file for running astyle to "beautify" c++ code
2 2
 # run using `astyle --options=.astylerc src/*.{cc,cpp,h}`
3 3
 
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-# don't create suffixes
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-suffix=none
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-
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-# use the google style of braces
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-style=google
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-
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 # use 4 spaces instead of tabs
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 indent=spaces=4
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 convert-tabs
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-# indent 'class' and 'switch' blocks
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-indent-classes
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-indent-switches
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-
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-# empty lines around blocks, labels, class, closing headers, ...
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-break-blocks=all
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-
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-# spaces around operator
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-pad-oper
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-
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 # remove spaces in and around parenthesis except in front of headers
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 # Example: foo ( bar, baz ); -> foo(bar, baz);
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 unpad-paren
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@@ -28,9 +12,6 @@ unpad-paren
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 # insert a space after if, while, for, etc (exception to previous rule)
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 pad-header
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-# delete empty lines not created by `break-blocks=all`
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-delete-empty-lines
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-
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 # pointer and reference operators to name
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 align-pointer=name
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... ...
@@ -41,9 +22,5 @@ add-brackets
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 # use linux line-endings
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 lineend=linux
43 24
 
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-# why not keep the date the same?
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-# although the date is modified by micro seconds to force compile
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-preserve-date
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-
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 # restrict lines to 80 characters
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 max-code-length=120
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@@ -4,15 +4,7 @@
4 4
 
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 # ignore compiled files
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 *.so
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-*.o*
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-*.sw?
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-*.dll
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-
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-# ignore R data
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-*.RDS
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-
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-# ignore PDFs
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-*.pdf
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+*.o
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17 9
 # ignore OS X files
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 *.DS_Store
... ...
@@ -2,9 +2,8 @@ Package: CoGAPS
2 2
 Version: 2.99.0
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 Date: 2014-08-23
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 Title: Coordinated Gene Activity in Pattern Sets
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-Author: Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey, Genevieve
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-    Stein-O'Brien, Michael Considine, John Stansfield, Shawn Sivy, Carlo Colantuoni,
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-    Alexander Favorov, Mike Ochs, Elana Fertig
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+Author: Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian,
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+    Jacob Carey, Genevieve Stein-O'Brien, Michael Considine, John Stansfield, Shawn Sivy, Carlo Colantuoni, Alexander Favorov, Mike Ochs, Elana Fertig
8 7
 Description: Coordinated Gene Activity in Pattern Sets (CoGAPS)
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     implements a Bayesian MCMC matrix factorization algorithm,
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     GAPS, and links it to gene set statistic methods to infer biological
... ...
@@ -27,8 +26,6 @@ Imports:
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     utils,
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     doParallel,
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     foreach,
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-    iterators,
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-    parallel,
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     ggplot2,
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     reshape2
34 31
 Suggests:
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@@ -51,7 +51,6 @@
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 #'@param fixedPatterns matrix of fixed values in either A or P matrix
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 #'@param whichMatrixFixed character to indicate whether A or P matrix
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 #'  contains the fixed patterns
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-#'@param checkpoint_file_name name of file to store checkpoint
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 #'@param checkpoint_interval time (in seconds) between cogaps checkpoints
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 #'@export
57 56
 
... ...
@@ -142,7 +141,14 @@ gapsRun <- function(D, S, ABins = data.frame(), PBins = data.frame(),
142 141
     return(cogapResult);
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 }
144 143
 
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+# TODO: remove dependency on D,S matrices
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+#' Restart Run from Checkpoint File
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 #' @export
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+#'
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+#' @param D data matrix
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+#' @param S uncertainty matrix
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+#' @param path path to checkpoint file
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+#' @return list containing information about A and P matrix
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 gapsRunFromCheckpoint <- function(D, S, path)
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 {
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     # call to C++ Rcpp code
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deleted file mode 100644
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@@ -1,28 +0,0 @@
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-# get directory of script
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-initial.options <- commandArgs(trailingOnly = FALSE)
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-file.arg.name <- "--file="
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-script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
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-script.basename <- dirname(script.name)
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-
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-# load packages
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-library(microbenchmark)
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-library(CoGAPS)
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-
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-# load benchmarks
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-source(paste(sep="/", script.basename, "cogaps.R"))
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-
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-# display package version
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-print(packageVersion('CoGAPS'))
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-
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-# run benchmarks
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-data(GIST_TS_20084)
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-nIter <- 3000
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-print(runCogapsBenchmark(
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-    D=GIST.D[1:75,],
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-    S=GIST.S[1:75,],
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-    nEquil=nIter,
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-    nSample=nIter,
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-    nFactor=7,
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-    seed=12345,
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-    reps=10
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-))
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\ No newline at end of file
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deleted file mode 100644
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@@ -1,13 +0,0 @@
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-library(CoGAPS)
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-library(microbenchmark)
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-
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-runCogapsBenchmark <- function(D, S, nEquil, nSample, nFactor, seed, reps)
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-{
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-    return(microbenchmark(gapsRun(D, S,
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-        nEquil=nEquil,
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-        nSample=nSample,
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-        nFactor=nFactor,
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-        seed=seed,
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-        messages=FALSE),
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-    times=reps))
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-}
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\ No newline at end of file
... ...
@@ -71,8 +71,6 @@ domain for relative probabilities}
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 contains the fixed patterns}
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 \item{checkpoint_interval}{time (in seconds) between cogaps checkpoints}
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-
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-\item{checkpoint_file_name}{name of file to store checkpoint}
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 }
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 \description{
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 \code{gapsRun} calls the C++ MCMC code and performs Bayesian
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new file mode 100644
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@@ -0,0 +1,22 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/gapsRun.R
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+\name{gapsRunFromCheckpoint}
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+\alias{gapsRunFromCheckpoint}
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+\title{Restart Run from Checkpoint File}
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+\usage{
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+gapsRunFromCheckpoint(D, S, path)
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+}
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+\arguments{
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+\item{D}{data matrix}
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+
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+\item{S}{uncertainty matrix}
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+
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+\item{path}{path to checkpoint file}
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+}
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+\value{
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+list containing information about A and P matrix
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+}
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+\description{
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+Restart Run from Checkpoint File
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+}
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+
... ...
@@ -144,7 +144,7 @@ AtomicProposal AtomicSupport::makeProposal() const
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     }
145 145
 
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     float unif = gaps::random::uniform();
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-    if ((mNumAtoms < 2 && unif <= 0.6667) || unif <= 0.5) // birth/death
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+    if ((mNumAtoms < 2 && unif <= 0.6667f) || unif <= 0.5f) // birth/death
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     {
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         if (mNumAtoms >= mMaxNumAtoms)
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         {
... ...
@@ -8,7 +8,6 @@
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 #include <fstream>
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 #include <vector>
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 #include <stdint.h>
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-//#include <boost/serialization/map.hpp>
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 struct AtomicProposal
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 {
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@@ -31,6 +30,18 @@ struct AtomicProposal
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     {}
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 };
33 32
 
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+struct Atom
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+{
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+    uint64_t pos;
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+    float mass;
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+};
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+
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+struct AtomNeighbors
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+{
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+    Atom left;
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+    Atom right;
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+};
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+
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 class AtomicSupport 
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 {
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 private:
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@@ -43,6 +54,8 @@ public:
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     char mLabel;
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     // storage of the atomic domain
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+    //std::vector<Atom> mAtoms;
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+    //std::map<uint64_t, uint64_t> mAtomPositions;
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     std::map<uint64_t, float> mAtomicDomain;
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     uint64_t mNumAtoms;
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     uint64_t mMaxNumAtoms;
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@@ -62,6 +75,11 @@ public:
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     // expected magnitude of each atom (must be > 0)
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     float mLambda;
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+    // functions for dealing with atomic data structure
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+    //void addAtom(Atom atom); // O(logN)
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+    //void removeAtom(Atom atom); // O(logN)
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+    //AtomNeighbors getNeighbors(uint64_t pos); // O(logN)
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+
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     // convert atomic position to row/col of the matrix
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     uint64_t getRow(uint64_t pos) const;
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     uint64_t getCol(uint64_t pos) const;
... ...
@@ -24,7 +24,7 @@ static bpt::ptime lastCheckpoint;
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 static void createCheckpoint(GapsInternalState &state)
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 {
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     state.numCheckpoints++;
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-    std::cout << "creating gaps checkpoint...";
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+    Rcpp::Rcout << "creating gaps checkpoint...";
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     bpt::ptime start = bpt::microsec_clock::local_time();
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     Archive ar("gaps_checkpoint_" + SSTR(state.numCheckpoints) + ".out",
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         ARCHIVE_WRITE);
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@@ -39,7 +39,7 @@ static void createCheckpoint(GapsInternalState &state)
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     ar.close();
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     bpt::time_duration diff = bpt::microsec_clock::local_time() - start;
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     double elapsed = diff.total_milliseconds() / 1000.;
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-    std::cout << " finished in " << elapsed << " seconds\n";
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+    Rcpp::Rcout << " finished in " << elapsed << " seconds\n";
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 }
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 static void runGibbsSampler(GapsInternalState &state, unsigned nIterTotal,
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@@ -92,7 +92,7 @@ Vector &chi2Vec, Vector &aAtomVec, Vector &pAtomVec)
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             if ((state.iter + 1) % state.nOutputs == 0 && state.messages)
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             {
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                 std::string temp = state.phase == GAPS_CALIBRATION ? "Equil: " : "Samp: ";
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-                std::cout << temp << state.iter + 1 << " of " << nIterTotal
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+                Rcpp::Rcout << temp << state.iter + 1 << " of " << nIterTotal
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                     << ", Atoms:" << aAtomVec[state.iter] << "(" << pAtomVec[state.iter]
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                     << ") Chi2 = " << state.sampler.chi2() << '\n';
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             }
... ...
@@ -187,7 +187,7 @@ Rcpp::List cogapsFromCheckpoint(const std::string &fileName)
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     ar >> magicNum;
188 188
     if (magicNum != ARCHIVE_MAGIC_NUM)
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     {
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-        std::cout << "invalid checkpoint file" << std::endl;
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+        Rcpp::Rcout << "invalid checkpoint file" << std::endl;
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         return Rcpp::List::create();
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     }
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@@ -1,4 +1,4 @@
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-PKG_CPPFLAGS = -Wall -Wextra -O2
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+PKG_CPPFLAGS = -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0
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 OBJECTS =   Algorithms.o \
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             AtomicSupport.o \
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             Cogaps.o \
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@@ -6,8 +6,6 @@
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 #include <Rcpp.h>
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 #include <vector>
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-// use CRTP for different matrix types?
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-
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 // temporary: used for testing performance of float vs double
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 typedef float matrix_data_t;
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@@ -7,20 +7,15 @@
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 #include <boost/random/normal_distribution.hpp>
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 #include <boost/random/poisson_distribution.hpp>
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 #include <boost/random/exponential_distribution.hpp>
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-
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 #include <boost/random/mersenne_twister.hpp>
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-// need -O0 to run in valgrind, -O2 for performance
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-#pragma GCC push_options
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-#pragma GCC optimize ("O2")
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 #include <boost/math/distributions/normal.hpp>
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 #include <boost/math/distributions/exponential.hpp>
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 #include <boost/math/distributions/gamma.hpp>
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-#pragma GCC pop_options
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21 16
 #include <stdint.h>
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-#define Q_GAMMA_THRESHOLD 1E-6
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+#define Q_GAMMA_THRESHOLD 0.000001f
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 #define Q_GAMMA_MIN_VALUE 0.0
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 typedef boost::random::mt19937 RNGType;
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@@ -8,6 +8,8 @@
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  *  Distributed under the Boost Software License, Version 1.0. (See accompanying
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  *  file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
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  */
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+#include <Rcpp.h>
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+
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 #ifndef TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED
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 #define TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED
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... ...
@@ -7705,10 +7707,10 @@ namespace Catch {
7705 7707
 
7706 7708
 #ifndef CATCH_CONFIG_NOSTDOUT // If you #define this you must implement these functions
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     std::ostream& cout() {
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-        return std::cout;
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+        return Rcpp::Rcout;
7709 7711
     }
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     std::ostream& cerr() {
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-        return std::cerr;
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+        return Rcpp::Rcerr;
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     }
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     std::ostream& clog() {
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         return std::clog;