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CHECK report for sights on tokay2

This page was generated on 2019-10-16 12:36:05 -0400 (Wed, 16 Oct 2019).

Package 1517/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sights 1.10.0
Elika Garg
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/sights
Branch: RELEASE_3_9
Last Commit: a7e8ca2
Last Changed Date: 2019-05-02 11:54:02 -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 [ WARNINGS ] 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: sights
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sights.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings sights_1.10.0.tar.gz
StartedAt: 2019-10-16 07:08:05 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:11:06 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 180.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: sights.Rcheck
Warnings: 1

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:sights.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings sights_1.10.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/sights.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 'sights/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sights' version '1.10.0'
* 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 'sights' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMXbdtC/R.INSTALL132024e76ee6/sights/man/plotIGFit.Rd:19: file link 'geom_step' in package 'ggplot2' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/sights.Rcheck/00install.out' for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 R/sysdata.rda ... 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/sights.Rcheck/00check.log'
for details.



Installation output

sights.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/sights_1.10.0.tar.gz && rm -rf sights.buildbin-libdir && mkdir sights.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sights.buildbin-libdir sights_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL sights_1.10.0.zip && rm sights_1.10.0.tar.gz sights_1.10.0.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 2443k  100 2443k    0     0  18.9M      0 --:--:-- --:--:-- --:--:-- 20.0M

install for i386

* installing *source* package 'sights' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sights'
    finding HTML links ... done
    ex_dataMatrix                           html  
    inglese                                 html  
    normLoess                               html  
    normMedFil                              html  
    normR                                   html  
    normRobZ                                html  
    normSPAWN                               html  
    normSights                              html  
    normZ                                   html  
    plot3d                                  html  
    plotAutoco                              html  
    plotBox                                 html  
    plotHeatmap                             html  
    plotHist                                html  
    plotIGFit                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpMXbdtC/R.INSTALL132024e76ee6/sights/man/plotIGFit.Rd:19: file link 'geom_step' in package 'ggplot2' does not exist and so has been treated as a topic
    plotScatter                             html  
    plotSights                              html  
    statFDR                                 html  
    statRVM                                 html  
    statSights                              html  
    statT                                   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 'sights' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sights' as sights_1.10.0.zip
* DONE (sights)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'sights' successfully unpacked and MD5 sums checked

Tests output

sights.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(sights)
> test_check("sights") 
alpha= 2.527861 beta= 2.054019 
alpha= 2.162155 beta= 2.810248 
alpha= 2.162155 beta= 2.810248 
alpha= 2.162155 beta= 2.810248 
== testthat results  ===========================================================
[ OK: 65 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  48.37    1.46   49.82 

sights.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(sights)
> test_check("sights") 
alpha= 2.527861 beta= 2.054019 
alpha= 2.162155 beta= 2.810248 
alpha= 2.162155 beta= 2.810248 
alpha= 2.162155 beta= 2.810248 
== testthat results  ===========================================================
[ OK: 65 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  43.32    0.93   44.23 

Example timings

sights.Rcheck/examples_i386/sights-Ex.timings

nameusersystemelapsed
ex_dataMatrix0.040.000.03
inglese0.060.000.06
normLoess0.150.000.16
normMedFil0.160.000.16
normR0.030.000.03
normRobZ0.020.000.01
normSPAWN0.040.000.05
normSights000
normZ000
plot3d0.80.00.8
plotAutoco2.240.002.23
plotBox0.730.010.75
plotHeatmap1.360.021.38
plotHist0.300.000.29
plotIGFit0.210.000.22
plotScatter0.960.010.97
plotSights1.290.021.31
statFDR0.040.010.05
statRVM0.010.000.01
statSights0.020.000.02
statT0.040.000.05

sights.Rcheck/examples_x64/sights-Ex.timings

nameusersystemelapsed
ex_dataMatrix0.030.000.03
inglese0.070.010.08
normLoess0.160.030.19
normMedFil0.120.000.13
normR0.020.020.03
normRobZ000
normSPAWN0.050.000.05
normSights0.020.000.02
normZ000
plot3d1.150.001.15
plotAutoco303
plotBox1.440.001.44
plotHeatmap2.280.002.29
plotHist0.460.000.45
plotIGFit0.290.000.30
plotScatter1.110.021.12
plotSights1.630.001.63
statFDR0.040.020.06
statRVM0.020.000.01
statSights0.030.000.04
statT0.050.000.04