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CHECK report for IWTomics on tokay2

This page was generated on 2018-10-17 08:43:13 -0400 (Wed, 17 Oct 2018).

Package 766/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IWTomics 1.4.0
Marzia A Cremona
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/IWTomics
Branch: RELEASE_3_7
Last Commit: 5a1ef58
Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: IWTomics
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IWTomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings IWTomics_1.4.0.tar.gz
StartedAt: 2018-10-17 02:54:42 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:00:23 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 341.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: IWTomics.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IWTomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings IWTomics_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/IWTomics.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.4.0'
* 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-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:60: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:135: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:168: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:308: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:309: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsTest.Rd:61: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsTest.Rd:64: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsTest.Rd:79: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsTest.Rd:80: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/plot-IWTomicsData.Rd:96: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/regions_example.Rd:19: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/regions_example.Rd:15: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/smooth-IWTomicsData.Rd:78: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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
* 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
IWTomicsTest       46.36   0.83   47.19
IWTomics-package   10.59   1.98   13.05
IWTomicsData-class 10.34   0.05   10.96
plotSummary         6.63   0.06    6.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
IWTomicsTest       65.20   1.62   66.84
IWTomics-package   11.28   1.58   12.86
IWTomicsData-class 10.32   0.02   10.33
plotSummary         7.25   0.25    7.51
plotTest            5.02   0.44    5.46
* 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 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/IWTomics.Rcheck/00check.log'
for details.



Installation output

IWTomics.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/IWTomics_1.4.0.tar.gz && rm -rf IWTomics.buildbin-libdir && mkdir IWTomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IWTomics.buildbin-libdir IWTomics_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL IWTomics_1.4.0.zip && rm IWTomics_1.4.0.tar.gz IWTomics_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  682k  100  682k    0     0  11.3M      0 --:--:-- --:--:-- --:--:-- 12.8M

install for i386

* installing *source* package 'IWTomics' ...
** R
** data
** inst
** byte-compile and prepare 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-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:60: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:135: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:168: file link 'read.delim' in package 'utils' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:308: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsData-class.Rd:309: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
    IWTomicsTest                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsTest.Rd:61: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsTest.Rd:64: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsTest.Rd:79: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/IWTomicsTest.Rd:80: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
    features_example                        html  
    plot-IWTomicsData                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/plot-IWTomicsData.Rd:96: file link 'smooth' in package 'IWTomics' does not exist and so has been treated as a topic
    plotSummary                             html  
    plotTest                                html  
    regionsFeatures_center                  html  
    regionsFeatures_scale                   html  
    regions_example                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/regions_example.Rd:19: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/regions_example.Rd:15: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    smooth-IWTomicsData                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpcTxKig/R.INSTALL17246cd919/IWTomics/man/smooth-IWTomicsData.Rd:78: file link 'plot' in package 'IWTomics' does not exist and so has been treated as a topic
** 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_1.4.0.zip
* DONE (IWTomics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'IWTomics' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

IWTomics.Rcheck/examples_i386/IWTomics-Ex.timings

nameusersystemelapsed
ETn_example0.150.060.22
IWTomics-package10.59 1.9813.05
IWTomicsData-class10.34 0.0510.96
IWTomicsTest46.36 0.8347.19
features_example000
plot-IWTomicsData0.680.000.69
plotSummary6.630.066.68
plotTest3.530.063.60
regionsFeatures_center000
regionsFeatures_scale0.000.020.01
regions_example000
smooth-IWTomicsData1.410.031.44

IWTomics.Rcheck/examples_x64/IWTomics-Ex.timings

nameusersystemelapsed
ETn_example0.160.010.17
IWTomics-package11.28 1.5812.86
IWTomicsData-class10.32 0.0210.33
IWTomicsTest65.20 1.6266.84
features_example000
plot-IWTomicsData0.500.030.53
plotSummary7.250.257.51
plotTest5.020.445.46
regionsFeatures_center000
regionsFeatures_scale0.000.020.01
regions_example000
smooth-IWTomicsData1.660.061.72