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CHECK report for heatmaps on tokay2

This page was generated on 2019-10-16 12:38:27 -0400 (Wed, 16 Oct 2019).

Package 746/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
heatmaps 1.8.0
Malcolm Perry
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/heatmaps
Branch: RELEASE_3_9
Last Commit: 78d98cd
Last Changed Date: 2019-05-02 11:54:07 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: heatmaps
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:heatmaps.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings heatmaps_1.8.0.tar.gz
StartedAt: 2019-10-16 04:22:27 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:25:21 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 174.5 seconds
RetCode: 0
Status:  OK  
CheckDir: heatmaps.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:heatmaps.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings heatmaps_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/heatmaps.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'heatmaps/DESCRIPTION' ... OK
* this is package 'heatmaps' version '1.8.0'
* 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 'heatmaps' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   6.9Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeGaussian2D: no visible binding for global variable 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
* 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
** running examples for arch 'x64' ... OK
* 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-3.9-bioc/meat/heatmaps.Rcheck/00check.log'
for details.



Installation output

heatmaps.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/heatmaps_1.8.0.tar.gz && rm -rf heatmaps.buildbin-libdir && mkdir heatmaps.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=heatmaps.buildbin-libdir heatmaps_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL heatmaps_1.8.0.zip && rm heatmaps_1.8.0.tar.gz heatmaps_1.8.0.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 6698k  100 6698k    0     0  54.9M      0 --:--:-- --:--:-- --:--:-- 58.4M

install for i386

* installing *source* package 'heatmaps' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'scale' in package 'heatmaps'
** help
*** installing help indices
  converting help for package 'heatmaps'
    finding HTML links ... done
    CoverageHeatmap                         html  
    Heatmap-class                           html  
    Heatmap                                 html  
    HeatmapExamples                         html  
    PWMScanHeatmap                          html  
    PatternHeatmap                          html  
    coords                                  html  
    default_color                           html  
    getScale                                html  
    heatmapOptions                          html  
    image                                   html  
    label                                   html  
    length-Heatmap-method                   html  
    metadata                                html  
    nseq                                    html  
    plotHeatmap                             html  
    plotHeatmapList                         html  
    plotHeatmapMeta                         html  
    plotPatternDensityMap                   html  
    plot_clusters                           html  
    plot_legend                             html  
    rev-Heatmap-method                      html  
    scale                                   html  
    smoothHeatmap                           html  
    width-Heatmap-method                    html  
    xm                                      html  
    ym                                      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 'heatmaps' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'heatmaps' as heatmaps_1.8.0.zip
* DONE (heatmaps)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'heatmaps' successfully unpacked and MD5 sums checked

Tests output

heatmaps.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(heatmaps)

Attaching package: 'heatmaps'

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

    scale

> 
> test_check("heatmaps")
== testthat results  ===========================================================
[ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   5.03    0.43    5.43 

heatmaps.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(heatmaps)

Attaching package: 'heatmaps'

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

    scale

> 
> test_check("heatmaps")
== testthat results  ===========================================================
[ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   4.98    0.17    5.14 

Example timings

heatmaps.Rcheck/examples_i386/heatmaps-Ex.timings

nameusersystemelapsed
CoverageHeatmap0.200.030.23
Heatmap-class0.020.000.02
Heatmap0.020.000.01
PWMScanHeatmap0.030.000.03
PatternHeatmap0.050.000.05
coords0.010.000.02
default_color000
getScale000
heatmapOptions000
image0.020.000.01
label0.010.000.02
metadata000
nseq0.020.000.01
plotHeatmap0.330.000.33
plotHeatmapList0.080.000.08
plotHeatmapMeta0.030.000.03
plotPatternDensityMap0.260.010.28
plot_clusters0.080.000.08
plot_legend0.030.000.03
scale0.020.000.02
smoothHeatmap0.040.020.06
xm0.020.020.03
ym0.020.000.02

heatmaps.Rcheck/examples_x64/heatmaps-Ex.timings

nameusersystemelapsed
CoverageHeatmap0.130.000.13
Heatmap-class000
Heatmap000
PWMScanHeatmap0.030.000.03
PatternHeatmap0.050.010.06
coords000
default_color000
getScale000
heatmapOptions000
image0.020.000.01
label000
metadata0.020.000.02
nseq0.010.000.01
plotHeatmap0.330.000.33
plotHeatmapList0.050.020.06
plotHeatmapMeta0.030.000.03
plotPatternDensityMap0.440.050.49
plot_clusters0.030.030.06
plot_legend0.020.000.01
scale000
smoothHeatmap0.020.010.03
xm0.010.000.02
ym000