diff --git a/cran-comments.md b/cran-comments.md index 53e512b62..f252fcf53 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,6 @@ ## Test environments -* local OS X install, R 3.1.2 -* ubuntu 12.04 (on travis-ci), R 3.1.2 +* local OS X install, R 3.2.0 +* ubuntu 12.04 (on travis-ci), R 3.2.0 * win-builder (devel and release) ## R CMD check results @@ -24,13 +24,15 @@ There were 2 NOTEs: These are needed because devtools simulates package loading, and hence needs to attach environments to the search path. - ## Downstream dependencies -I have also run R CMD check on all 28 downstream dependencies of devtools +I have also run R CMD check on all 29 downstream dependencies of devtools (https://github.com/hadley/devtools/blob/master/revdep/summary.md): +* There were 2 failures: + + * REDCapR: This looks to be an SSL connection problem + * NMF: this failed in the same way previously. + * As far as I can tell, there were no new failures related to changes in devtools. -* There was 1 failure: REDCapR. This looks to be an SSL connection problem - so I don't believe it's related to the devtools update. diff --git a/revdep/check.R b/revdep/check.R index c5ca5c689..73a09931b 100644 --- a/revdep/check.R +++ b/revdep/check.R @@ -1,7 +1,7 @@ library("devtools") # Suggesting devtools probably just means that they're using it for -# development, so we're probably save skipping them. +# development, so we're probably safe skipping them. res <- revdep_check() revdep_check_save_summary(res) diff --git a/revdep/summary.md b/revdep/summary.md index 112d81bc9..9637146ee 100644 --- a/revdep/summary.md +++ b/revdep/summary.md @@ -6,7 +6,7 @@ |:--------|:----------------------------| |version |R version 3.2.0 (2015-04-16) | |system |x86_64, darwin13.4.0 | -|ui |RStudio (0.99.423) | +|ui |RStudio (0.99.430) | |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Chicago | @@ -17,13 +17,13 @@ |:----------|:--|:--------|:----------|:--------------| |digest | |0.6.8 |2014-12-31 |CRAN (R 3.2.0) | |evaluate | |0.7 |2015-04-21 |CRAN (R 3.2.0) | -|git2r | |0.7 |2015-02-23 |CRAN (R 3.2.0) | +|git2r | |0.10.1 |2015-05-07 |CRAN (R 3.2.0) | |httr | |0.6.1 |2015-01-01 |CRAN (R 3.2.0) | |jsonlite | |0.9.16 |2015-04-11 |CRAN (R 3.2.0) | -|knitr | |1.10 |2015-04-23 |CRAN (R 3.2.0) | +|knitr | |1.10.5 |2015-05-06 |CRAN (R 3.2.0) | |lintr | |0.2.0 |2014-12-01 |CRAN (R 3.2.0) | |memoise | |0.2.1 |2014-04-22 |CRAN (R 3.2.0) | -|Rcpp | |0.11.5 |2015-03-06 |CRAN (R 3.2.0) | +|Rcpp | |0.11.6 |2015-05-01 |CRAN (R 3.2.0) | |RCurl | |1.95-4.6 |2015-04-24 |CRAN (R 3.2.0) | |rmarkdown | |0.5.1 |2015-01-26 |CRAN (R 3.2.0) | |roxygen2 | |4.1.1 |2015-04-15 |CRAN (R 3.2.0) | @@ -33,7 +33,7 @@ |whisker | |0.3-2 |2013-04-28 |CRAN (R 3.2.0) | # Check results -27 checked out of 28 dependencies +28 checked out of 29 dependencies ## aRxiv (0.5.8) Maintainer: Karl Broman @@ -72,7 +72,7 @@ Maintainer: Sten Ilmjarv ``` checking package dependencies ... ERROR -Packages required but not available: ‘R.utils’ ‘affxparser’ ‘affy’ ‘oligo’ +Packages required but not available: ‘affxparser’ ‘affy’ ‘oligo’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -107,6 +107,11 @@ DONE Status: 3 NOTEs ``` +## FedData (1.1.0) +Maintainer: R. Kyle Bocinsky + +__OK__ + ## gender (0.4.3) Maintainer: Lincoln Mullen Bug reports: https://github.com/ropensci/gender/issues @@ -163,15 +168,11 @@ __OK__ Maintainer: Sean C. Anderson Bug reports: http://github.com/seananderson/metafolio/issues -``` -checking package dependencies ... NOTE -Package suggested but not available for checking: ‘TeachingDemos’ -``` ``` checking whether package ‘metafolio’ can be installed ... ERROR Installation failed. -See ‘/private/tmp/Rtmpm9ZW8z/check_cranea40497c6391/metafolio.Rcheck/00install.out’ for details. -Status: 1 ERROR, 1 NOTE +See ‘/private/tmp/RtmpwEmZkv/check_cran34e757c9c63b/metafolio.Rcheck/00install.out’ for details. +Status: 1 ERROR ``` ## myTAI (0.0.2) @@ -256,16 +257,11 @@ Running examples in ‘NMF-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: nmfModel -> ### Title: Factory Methods NMF Models -> ### Aliases: nmfModel nmfModel,data.frame,data.frame-method -> ### nmfModel,formula,ANY-method nmfModel,matrix,ANY-method -> ### nmfModel,matrix,matrix-method nmfModel-methods -> ### nmfModel,missing,ANY-method nmfModel,missing,missing-method -> ### nmfModel,NULL,ANY-method nmfModel,numeric,matrix-method -> ### nmfModel,numeric,missing-method nmfModel,numeric,numeric-method -> ### nmfModels -> ### Keywords: methods +> ### Name: NMF-package +> ### Title: Algorithms and framework for Nonnegative Matrix Factorization +> ### (NMF). +> ### Aliases: NMF NMF-package +> ### Keywords: package > > ### ** Examples > @@ -274,224 +270,17 @@ The error most likely occurred in: > options(R_CHECK_RUNNING_EXAMPLES_=TRUE) > ## End(Don't show) > -> #---------- -> # nmfModel,numeric,numeric-method -> #---------- -> # data -> n <- 20; r <- 3; p <- 10 -> V <- rmatrix(n, p) # some target matrix -> -> # create a r-ranked NMF model with a given target dimensions n x p as a 2-length vector -> nmfModel(r, c(n,p)) # directly - -features: 20 -basis/rank: 3 -samples: 10 -> nmfModel(r, dim(V)) # or from an existing matrix <=> nmfModel(r, V) - -features: 20 -basis/rank: 3 -samples: 10 -> # or alternatively passing each dimension separately -> nmfModel(r, n, p) - -features: 20 -basis/rank: 3 -samples: 10 -> -> # trying to create a NMF object based on incompatible matrices generates an error -> w <- rmatrix(n, r) -> h <- rmatrix(r+1, p) -> try( new('NMFstd', W=w, H=h) ) -Error in validObject(.Object) : - invalid class “NMFstd” object: Dimensions of W and H are not compatible [ncol(W)= 3 != nrow(H)= 4 ] -> try( nmfModel(w, h) ) -Error in .local(rank, target, ...) : - nmfModel - Invalid number of columns in the basis matrix [3]: it should match the number of rows in the mixture coefficient matrix [4] -> try( nmfModel(r+1, W=w, H=h) ) -Error in .local(rank, target, ...) : - nmfModel - Objective rank [4] is greater than the number of columns in W [3] -> # The factory method can be force the model to match some target dimensions -> # but warnings are thrown -> nmfModel(r, W=w, H=h) -Warning in .local(rank, target, ...) : - nmfModel - Objective rank [3] is lower than the number of rows in H [4]: only the first 3 rows of H will be used - -features: 20 -basis/rank: 3 -samples: 10 -> nmfModel(r, n-1, W=w, H=h) -Warning in .local(rank, target, ...) : - nmfModel - Number of rows in target is lower than the number of rows in W [20]: only the first 19 rows of W will be used -Warning in .local(rank, target, ...) : - nmfModel - Objective rank [3] is lower than the number of rows in H [4]: only the first 3 rows of H will be used - -features: 19 -basis/rank: 3 -samples: 10 -> -> #---------- -> # nmfModel,numeric,missing-method -> #---------- -> ## Empty model of given rank -> nmfModel(3) - -features: 0 -basis/rank: 3 -samples: 0 -> -> #---------- -> # nmfModel,missing,ANY-method -> #---------- -> nmfModel(target=10) #square - -features: 10 -basis/rank: 0 -samples: 10 -> nmfModel(target=c(10, 5)) - -features: 10 -basis/rank: 0 -samples: 5 -> -> #---------- -> # nmfModel,missing,missing-method -> #---------- -> # Build an empty NMF model -> nmfModel() - -features: 0 -basis/rank: 0 -samples: 0 -> -> # create a NMF object based on one random matrix: the missing matrix is deduced -> # Note this only works when using factory method NMF -> n <- 50; r <- 3; -> w <- rmatrix(n, r) -> nmfModel(W=w) - -features: 50 -basis/rank: 3 -samples: 0 -> -> # create a NMF object based on random (compatible) matrices -> p <- 20 -> h <- rmatrix(r, p) -> nmfModel(H=h) - -features: 0 -basis/rank: 3 -samples: 20 -> -> # specifies two compatible matrices -> nmfModel(W=w, H=h) - -features: 50 -basis/rank: 3 -samples: 20 -> # error if not compatible -> try( nmfModel(W=w, H=h[-1,]) ) -Error in .local(rank, target, ...) : - nmfModel - Invalid number of columns in the basis matrix [3]: it should match the number of rows in the mixture coefficient matrix [2] -> -> #---------- -> # nmfModel,numeric,matrix-method -> #---------- -> # create a r-ranked NMF model compatible with a given target matrix -> obj <- nmfModel(r, V) -> all(is.na(basis(obj))) -[1] TRUE -> -> #---------- -> # nmfModel,matrix,matrix-method -> #---------- -> ## From two existing factors -> -> # allows a convenient call without argument names -> w <- rmatrix(n, 3); h <- rmatrix(3, p) -> nmfModel(w, h) - -features: 50 -basis/rank: 3 -samples: 20 -> -> # Specify the type of NMF model (e.g. 'NMFns' for non-smooth NMF) -> mod <- nmfModel(w, h, model='NMFns') -> mod - -features: 50 -basis/rank: 3 -samples: 20 -theta: 0.5 -> -> # One can use such an NMF model as a seed when fitting a target matrix with nmf() -> V <- rmatrix(mod) -> res <- nmf(V, mod) -> nmf.equal(res, nmf(V, mod)) -[1] TRUE -> -> # NB: when called only with such a seed, the rank and the NMF algorithm -> # are selected based on the input NMF model. -> # e.g. here rank was 3 and the algorithm "nsNMF" is used, because it is the default -> # algorithm to fit "NMFns" models (See ?nmf). -> -> #---------- -> # nmfModel,matrix,ANY-method -> #---------- -> ## swapped arguments `rank` and `target` -> V <- rmatrix(20, 10) -> nmfModel(V) # equivalent to nmfModel(target=V) - -features: 20 -basis/rank: 0 -samples: 10 -> nmfModel(V, 3) # equivalent to nmfModel(3, V) - -features: 20 -basis/rank: 3 -samples: 10 -> -> #---------- -> # nmfModel,formula,ANY-method -> #---------- -> # empty 3-rank model -> nmfModel(~ 3) - -features: 0 -basis/rank: 3 -samples: 0 -> -> # 3-rank model that fits a given data matrix -> x <- rmatrix(20,10) -> nmfModel(x ~ 3) - -features: 20 -basis/rank: 3 -samples: 10 -> -> # add fixed coefficient term defined by a factor -> gr <- gl(2, 5) -> nmfModel(x ~ 3 + gr) - -features: 20 -basis/rank: 5 -samples: 10 -fixed coef [2]: - gr = <1, 2> +> # generate a synthetic dataset with known classes +> n <- 50; counts <- c(5, 5, 8); +> V <- syntheticNMF(n, counts) > -> # add fixed coefficient term defined by a numeric covariate -> nmfModel(x ~ 3 + gr + b, data=list(b=runif(10))) - -features: 20 -basis/rank: 6 -samples: 10 -fixed coef [3]: - gr = <1, 2> - b = 0.0101301828399301, 0.21454192395322, ..., 0.767450851621106 +> # perform a 3-rank NMF using the default algorithm +> res <- nmf(V, 3) > -> # 3-rank model that fits a given ExpressionSet (with fixed coef terms) -> e <- ExpressionSet(x) -Error: could not find function "ExpressionSet" +> basismap(res) +Error in process_tracks(x, tracks, annRow, annCol) : + Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'. +Calls: basismap -> basismap -> .local -> process_tracks Execution halted ``` ```