Package: TimeSeriesExperiment

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TimeSeriesExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TimeSeriesExperiment_1.4.0.tar.gz

StartedAt: 2020-04-15 07:05:31 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 07:11:29 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 357.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TimeSeriesExperiment.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TimeSeriesExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TimeSeriesExperiment_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TimeSeriesExperiment.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 'TimeSeriesExperiment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TimeSeriesExperiment' version '1.4.0'
* 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 'TimeSeriesExperiment' 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
Unexported object imported by a ':::' call: 'S4Vectors:::selectSome'
  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
clusterTimeSeries: no visible binding for global variable 'freq'
clusterTimeSeries: no visible binding for global variable '.'
Undefined global functions or variables:
  . freq
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotHeatmap':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
differentialExpression 11.49   0.01    11.5
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
differentialExpression 18.3      0   18.29
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/TimeSeriesExperiment.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TimeSeriesExperiment_1.4.0.tar.gz && rm -rf TimeSeriesExperiment.buildbin-libdir && mkdir TimeSeriesExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TimeSeriesExperiment.buildbin-libdir TimeSeriesExperiment_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TimeSeriesExperiment_1.4.0.zip && rm TimeSeriesExperiment_1.4.0.tar.gz TimeSeriesExperiment_1.4.0.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  625k  100  625k    0     0  6917k      0 --:--:-- --:--:-- --:--:-- 7273k

install for i386

* installing *source* package 'TimeSeriesExperiment' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TimeSeriesExperiment'
    finding HTML links ... done
    TimeSeriesExperiment                    html  
    finding level-2 HTML links ... done

    addLags                                 html  
    assignClusterDynamic                    html  
    assignClusterStatic                     html  
    clusterAssignment                       html  
    clusterData                             html  
    clusterTimeSeries                       html  
    colData                                 html  
    collapseReplicates                      html  
    collapsed-data                          html  
    dataToTimeSeries                        html  
    differentialExpression                  html  
    dimensionReduction                      html  
    dot-addLagsToTimeSeries                 html  
    dot-imputeData                          html  
    endoderm_small                          html  
    filterFeatures                          html  
    groups                                  html  
    makeTimeSeries                          html  
    makeTimeSeriesExperimentFromExpressionSet
                                            html  
    makeTimeSeriesExperimentFromSummarizedExperiment
                                            html  
    meltMatrix                              html  
    normalizeData                           html  
    pathwayEnrichment                       html  
    pipe                                    html  
    plotEnrichment                          html  
    plotHeatmap                             html  
    plotSamplePCA                           html  
    plotTimeSeries                          html  
    plotTimeSeriesClusters                  html  
    plotTimeSeriesPCA                       html  
    replicates                              html  
    rowData                                 html  
    row_and_colnames                        html  
    runPCA                                  html  
    show-methods                            html  
    timeSeries                              html  
    timepointDE                             html  
    timepoints                              html  
    trajectoryDE                            html  
    varianceStabilization                   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 'TimeSeriesExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TimeSeriesExperiment' as TimeSeriesExperiment_1.4.0.zip
* DONE (TimeSeriesExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TimeSeriesExperiment' successfully unpacked and MD5 sums checked