Multiple platform build/check report for BioC 3.11 - CHECK report for tradeSeq on tokay2

Package: tradeSeq

Version: 1.2.01

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tradeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings tradeSeq_1.2.01.tar.gz

StartedAt: 2020-10-17 08:57:43 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 09:20:28 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 1364.5 seconds

RetCode: 0

Status: OK

CheckDir: tradeSeq.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tradeSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings tradeSeq_1.2.01.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/tradeSeq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.2.01'
* 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'
.findKnots: no visible binding for global variable 't1'
.findKnots: no visible binding for global variable 'l1'
.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,CellDataSet: no visible binding for global variable '.'
fitGAM,CellDataSet: no visible binding for global variable 'V1'
fitGAM,CellDataSet : <anonymous>: no visible binding for global
  variable 'Y'
fitGAM,CellDataSet: no visible global function definition for
  'bind_cols'
fitGAM,CellDataSet: no visible binding for global variable 'cds'
Undefined global functions or variables:
  . V1 X1 X2 Y bind_cols cds dim1 dim2 gene_count 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 (user + system) or elapsed time > 5s
                           user system elapsed
associationTest           71.92   1.67   82.91
fitGAM                    61.51   0.29   63.70
plotGeneCount             53.11   0.21   53.39
evaluateK                 32.34   0.19   36.37
clusterExpressionPatterns 11.58   0.03   11.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
associationTest           67.86   0.37   68.29
fitGAM                    61.55   0.13   61.78
plotGeneCount             53.33   0.19   53.52
evaluateK                 26.48   0.07   26.65
clusterExpressionPatterns  9.39   0.04    9.43
* 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-3.11-bioc/meat/tradeSeq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/tradeSeq_1.2.01.tar.gz && rm -rf tradeSeq.buildbin-libdir && mkdir tradeSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tradeSeq.buildbin-libdir tradeSeq_1.2.01.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL tradeSeq_1.2.01.zip && rm tradeSeq_1.2.01.tar.gz tradeSeq_1.2.01.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
100 10.2M  100 10.2M    0     0  38.5M      0 --:--:-- --:--:-- --:--:-- 39.6M

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  
    nknots                                  html  
    patternTest                             html  
    plotGeneCount                           html  
    plotSmoothers                           html  
    predictCells                            html  
    predictSmooth                           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_1.2.01.zip
* DONE (tradeSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'tradeSeq' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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


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
> 
> test_check("tradeSeq")
== testthat results  ===========================================================
[ OK: 84 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 216.67    2.43  220.35


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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


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
> 
> test_check("tradeSeq")
== testthat results  ===========================================================
[ OK: 84 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 222.85    1.20  224.14

name	user	system	elapsed
associationTest	71.92	1.67	82.91
clusterExpressionPatterns	11.58	0.03	11.69
diffEndTest	0.03	0.00	0.03
earlyDETest	0.05	0.00	0.05
evaluateK	32.34	0.19	36.37
fitGAM	61.51	0.29	63.70
getSmootherPvalues	0.07	0.00	0.07
getSmootherTestStats	0.06	0.00	0.06
nknots	0.02	0.00	0.01
patternTest	0.03	0.00	0.04
plotGeneCount	53.11	0.21	53.39
plotSmoothers	0.41	0.00	0.41
predictCells	0.01	0.00	0.01
predictSmooth	0.03	0.00	0.04
startVsEndTest	0.05	0.00	0.04

name	user	system	elapsed
associationTest	67.86	0.37	68.29
clusterExpressionPatterns	9.39	0.04	9.43
diffEndTest	0.03	0.00	0.03
earlyDETest	0.04	0.00	0.03
evaluateK	26.48	0.07	26.65
fitGAM	61.55	0.13	61.78
getSmootherPvalues	0.06	0.00	0.06
getSmootherTestStats	0.05	0.00	0.05
nknots	0.01	0.00	0.01
patternTest	0.05	0.02	0.06
plotGeneCount	53.33	0.19	53.52
plotSmoothers	0.43	0.00	0.43
predictCells	0.04	0.00	0.03
predictSmooth	0.04	0.00	0.05
startVsEndTest	0.06	0.00	0.06

CHECK report for tradeSeq on tokay2

Summary

Command output

Installation output

Tests output

Example timings