Package: tradeSeq

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tradeSeq_1.0.1.tar.gz

StartedAt: 2020-04-15 06:13:53 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:23:01 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 547.5 seconds

RetCode: 0

Status:  OK

CheckDir: tradeSeq.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:tradeSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings tradeSeq_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/tradeSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tradeSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tradeSeq’ version ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tradeSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘mgcv:::s’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.earlyDETest: no visible binding for global variable ‘X1’
.earlyDETest: no visible binding for global variable ‘X2’
.fitGAM: no visible binding for global variable ‘t1’
.fitGAM: no visible binding for global variable ‘l1’
.fitGAM: no visible binding for global variable ‘X’
.fitGAM: no visible binding for global variable ‘dm’
.fitGAM: no visible binding for global variable ‘knotPoints’
.plotSmoothers: no visible binding for global variable ‘gene_count’
.plotSmoothers: no visible binding for global variable ‘lineage’
.plotSmoothers_sce: no visible binding for global variable ‘gene_count’
.plotSmoothers_sce: no visible binding for global variable ‘lineage’
plotGeneCount: no visible binding for global variable ‘dim1’
plotGeneCount: no visible binding for global variable ‘dim2’
fitGAM,matrix: no visible binding for global variable ‘X’
fitGAM,matrix: no visible binding for global variable ‘dm’
Undefined global functions or variables:
  X X1 X2 dim1 dim2 dm gene_count knotPoints l1 lineage t1
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
fitGAM                    65.263  4.864  74.416
plotGeneCount             53.448  3.321  62.545
evaluateK                 28.608  0.400  29.199
clusterExpressionPatterns 11.990  0.227  12.295
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/tradeSeq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL tradeSeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘tradeSeq’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tradeSeq)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(tradeSeq)
tradeSeq has been updated to accommodate singleCellExperiment objects as output, making it much more memory efficient. Please check the news file and the updated vignette for details.
> library(SingleCellExperiment)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

> library(slingshot)
Loading required package: princurve
> data("sds", package="tradeSeq")
> 
> set.seed(3)
> n <- nrow(reducedDim(sds))
> G <- 100
> pseudotime <- slingPseudotime(sds, na=FALSE)
> cellWeights <- slingCurveWeights(sds)
> means <- matrix(rep(rlnorm(n=G, meanlog=4, sdlog=1), n),
+                 nrow=G, ncol=n, byrow=FALSE)
> dispersions <- matrix(rep(runif(n=G, min=0.8, max=3), n),
+                       nrow=G, ncol=n, byrow=FALSE)
> # add pseudotime effects for a few
> id <- sample(1:100, 20)
> means[id,] <- sweep(means[id,],2,FUN="*",STATS=(pseudotime[,1]/50))
> # simulate NB counts
> counts <- matrix(rnbinom(n=G*n, mu=means, size=1/dispersions), nrow=G, ncol=n)
> 
> 
> # fitGAM tests
> set.seed(3)
> sdsFit <- tradeSeq::fitGAM(counts, sds, nknots=3, verbose=FALSE, parallel=FALSE)
> set.seed(3)
> listFit <- tradeSeq::fitGAM(counts, pseudotime = pseudotime,
+                             cellWeights = cellWeights, nknots = 3,
+                             verbose = FALSE, parallel = FALSE)
> 
> test_check("tradeSeq")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 54.312   1.199  55.914 

name	user	system	elapsed
associationTest	0.069	0.002	0.071
clusterExpressionPatterns	11.990	0.227	12.295
diffEndTest	0.053	0.001	0.055
earlyDETest	0.083	0.005	0.088
evaluateK	28.608	0.400	29.199
fitGAM	65.263	4.864	74.416
getSmootherPvalues	0.045	0.001	0.046
getSmootherTestStats	0.056	0.001	0.057
patternTest	0.081	0.001	0.083
plotGeneCount	53.448	3.321	62.545
plotSmoothers	0.522	0.003	0.531
startVsEndTest	0.073	0.001	0.076