Hector Roux de Bezieux
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/tradeSeq |
| Branch: RELEASE_3_10 |
| Last Commit: eb046aa |
| Last Changed Date: 2020-04-03 04:11:27 -0400 (Fri, 03 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:33:38 -0400 (Wed, 15 Apr 2020).
| Package 1743/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| tradeSeq 1.0.1 Hector Roux de Bezieux
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: tradeSeq |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tradeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings tradeSeq_1.0.1.tar.gz |
| StartedAt: 2020-04-15 07:10:11 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:24:35 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 864.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: tradeSeq.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tradeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings tradeSeq_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/tradeSeq.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitGAM 83.84 0.74 90.31
plotGeneCount 70.07 0.89 73.44
evaluateK 32.17 0.42 33.07
clusterExpressionPatterns 10.93 0.86 11.96
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitGAM 70.83 0.23 72.55
plotGeneCount 58.85 0.27 59.50
evaluateK 30.88 0.21 32.22
clusterExpressionPatterns 9.86 0.14 10.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.10-bioc/meat/tradeSeq.Rcheck/00check.log'
for details.
tradeSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/tradeSeq_1.0.1.tar.gz && rm -rf tradeSeq.buildbin-libdir && mkdir tradeSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tradeSeq.buildbin-libdir tradeSeq_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL tradeSeq_1.0.1.zip && rm tradeSeq_1.0.1.tar.gz tradeSeq_1.0.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
85 9596k 85 8192k 0 0 15.1M 0 --:--:-- --:--:-- --:--:-- 15.1M
100 9596k 100 9596k 0 0 17.3M 0 --:--:-- --:--:-- --:--:-- 17.3M
install for i386
* installing *source* package 'tradeSeq' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'tradeSeq'
finding HTML links ... done
associationTest html
celltype html
clusterExpressionPatterns html
finding level-2 HTML links ... done
countMatrix html
crv html
diffEndTest html
earlyDETest html
evaluateK html
fitGAM html
gamList html
getSmootherPvalues html
getSmootherTestStats html
patternTest html
plotGeneCount html
plotSmoothers html
sds html
startVsEndTest html
** 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
install for x64
* installing *source* package 'tradeSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tradeSeq' as tradeSeq_1.0.1.zip
* DONE (tradeSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'tradeSeq' successfully unpacked and MD5 sums checked
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tradeSeq.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
53.26 2.46 59.48
|
tradeSeq.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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
43.62 0.79 44.43
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tradeSeq.Rcheck/examples_i386/tradeSeq-Ex.timings
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tradeSeq.Rcheck/examples_x64/tradeSeq-Ex.timings
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