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CHECK report for IWTomics on tokay1

This page was generated on 2018-04-12 13:29:05 -0400 (Thu, 12 Apr 2018).

Package 726/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IWTomics 1.2.0
Marzia A Cremona
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/IWTomics
Branch: RELEASE_3_6
Last Commit: cf2d62c
Last Changed Date: 2017-10-30 12:41:23 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IWTomics
Version: 1.2.0
Command: rm -rf IWTomics.buildbin-libdir IWTomics.Rcheck && mkdir IWTomics.buildbin-libdir IWTomics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IWTomics.buildbin-libdir IWTomics_1.2.0.tar.gz >IWTomics.Rcheck\00install.out 2>&1 && cp IWTomics.Rcheck\00install.out IWTomics-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IWTomics.buildbin-libdir --install="check:IWTomics-install.out" --force-multiarch --no-vignettes --timings IWTomics_1.2.0.tar.gz
StartedAt: 2018-04-12 00:57:49 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:03:49 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 360.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: IWTomics.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf IWTomics.buildbin-libdir IWTomics.Rcheck && mkdir IWTomics.buildbin-libdir IWTomics.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IWTomics.buildbin-libdir IWTomics_1.2.0.tar.gz >IWTomics.Rcheck\00install.out 2>&1 && cp IWTomics.Rcheck\00install.out IWTomics-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IWTomics.buildbin-libdir --install="check:IWTomics-install.out" --force-multiarch --no-vignettes --timings IWTomics_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IWTomics.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IWTomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IWTomics' version '1.2.0'
* 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 'IWTomics' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:60: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:135: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:168: missing file link 'read.delim'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:308: missing file link 'plot'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:309: missing file link 'smooth'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsTest.Rd:61: missing file link 'smooth'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsTest.Rd:64: missing file link 'smooth'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsTest.Rd:79: missing file link 'plot'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsTest.Rd:80: missing file link 'smooth'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/plot-IWTomicsData.Rd:96: missing file link 'smooth'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/regions_example.Rd:19: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/regions_example.Rd:15: missing file link 'GRangesList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/smooth-IWTomicsData.Rd:78: missing file link 'plot'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IWTomics.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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
IWTomicsTest       51.02   0.62   51.67
IWTomics-package   17.37   1.16   18.53
IWTomicsData-class 10.42   0.03   10.46
plotSummary         6.58   0.01    6.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
IWTomicsTest       67.60   0.73   68.33
IWTomics-package   15.31   0.81   16.13
IWTomicsData-class 12.39   0.02   12.40
plotSummary        10.62   0.13   10.75
plotTest            5.19   0.01    5.22
* 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-3.6-bioc/meat/IWTomics.Rcheck/00check.log'
for details.

Installation output

IWTomics.Rcheck/00install.out


install for i386

* installing *source* package 'IWTomics' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'smooth' in package 'IWTomics'
** help
*** installing help indices
  converting help for package 'IWTomics'
    finding HTML links ... done
    ETn_example                             html  
    IWTomics-internal                       html  
    IWTomics-package                        html  
    IWTomicsData-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:60: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:135: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:168: missing file link 'read.delim'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:308: missing file link 'plot'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsData-class.Rd:309: missing file link 'smooth'
    IWTomicsTest                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsTest.Rd:61: missing file link 'smooth'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsTest.Rd:64: missing file link 'smooth'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsTest.Rd:79: missing file link 'plot'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/IWTomicsTest.Rd:80: missing file link 'smooth'
    features_example                        html  
    plot-IWTomicsData                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/plot-IWTomicsData.Rd:96: missing file link 'smooth'
    plotSummary                             html  
    plotTest                                html  
    regionsFeatures_center                  html  
    regionsFeatures_scale                   html  
    regions_example                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/regions_example.Rd:19: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/regions_example.Rd:15: missing file link 'GRangesList'
    smooth-IWTomicsData                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpM5TH53/R.INSTALL2b1041496a47/IWTomics/man/smooth-IWTomicsData.Rd:78: missing file link 'plot'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'IWTomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IWTomics' as IWTomics_1.2.0.zip
* DONE (IWTomics)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

IWTomics.Rcheck/examples_i386/IWTomics-Ex.timings

nameusersystemelapsed
ETn_example0.320.000.32
IWTomics-package17.37 1.1618.53
IWTomicsData-class10.42 0.0310.46
IWTomicsTest51.02 0.6251.67
features_example0.000.020.01
plot-IWTomicsData0.460.000.47
plotSummary6.580.016.60
plotTest4.030.034.07
regionsFeatures_center0.000.020.02
regionsFeatures_scale000
regions_example000
smooth-IWTomicsData1.230.021.25

IWTomics.Rcheck/examples_x64/IWTomics-Ex.timings

nameusersystemelapsed
ETn_example0.140.000.14
IWTomics-package15.31 0.8116.13
IWTomicsData-class12.39 0.0212.40
IWTomicsTest67.60 0.7368.33
features_example0.010.000.02
plot-IWTomicsData0.540.030.56
plotSummary10.62 0.1310.75
plotTest5.190.015.22
regionsFeatures_center000
regionsFeatures_scale0.020.000.02
regions_example000
smooth-IWTomicsData1.500.021.53