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CHECK report for nucleR on tokay1

This page was generated on 2019-04-13 11:21:43 -0400 (Sat, 13 Apr 2019).

Package 1067/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 2.14.0
Ricard Illa
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/nucleR
Branch: RELEASE_3_8
Last Commit: 28d33d4
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: nucleR
Version: 2.14.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nucleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings nucleR_2.14.0.tar.gz
StartedAt: 2019-04-13 04:12:30 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:18:28 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 357.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: nucleR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nucleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings nucleR_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/nucleR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nucleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nucleR' version '2.14.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'nucleR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:36: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:23: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:23: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:52: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/export.bed.Rd:28: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/export.bed.Rd:29: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/export.bed.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/fragmentLenDetect.Rd:27: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/mergeCalls.Rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/mergeCalls.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/peakScoring.Rd:63: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/plotPeaks.Rd:67: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processReads.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processReads.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processReads.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processReads.Rd:114: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processTilingArray.Rd:123: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/readBAM.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/readBowtie.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/nucleR.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
syntheticNucMap 24.72   0.09   24.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
syntheticNucMap 29.23   0.01   29.25
* 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-3.8-bioc/meat/nucleR.Rcheck/00check.log'
for details.



Installation output

nucleR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/nucleR_2.14.0.tar.gz && rm -rf nucleR.buildbin-libdir && mkdir nucleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nucleR.buildbin-libdir nucleR_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL nucleR_2.14.0.zip && rm nucleR_2.14.0.tar.gz nucleR_2.14.0.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  801k  100  801k    0     0  16.4M      0 --:--:-- --:--:-- --:--:-- 17.7M

install for i386

* installing *source* package 'nucleR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nucleR'
    finding HTML links ... done
    controlCorrection                       html  
    coverage.rpm                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:35: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:36: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:23: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:23: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/coverage.rpm.Rd:52: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
    export.bed                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/export.bed.Rd:28: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/export.bed.Rd:29: file link 'IRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/export.bed.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    export.wig                              html  
    filterFFT                               html  
    fragmentLenDetect                       html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/fragmentLenDetect.Rd:27: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    mergeCalls                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/mergeCalls.Rd:16: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/mergeCalls.Rd:28: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    nucleR-package                          html  
    nucleosome_htseq                        html  
    nucleosome_tiling                       html  
    pcKeepCompDetect                        html  
    peakDetection                           html  
    peakScoring                             html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/peakScoring.Rd:63: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    plotPeaks                               html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/plotPeaks.Rd:67: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
    processReads                            html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processReads.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processReads.Rd:54: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processReads.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processReads.Rd:114: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    processTilingArray                      html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/processTilingArray.Rd:123: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    readBAM                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/readBAM.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    readBowtie                              html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpaI46IF/R.INSTALL190c347b1af1/nucleR/man/readBowtie.Rd:16: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    syntheticNucMap                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'nucleR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nucleR' as nucleR_2.14.0.zip
* DONE (nucleR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'nucleR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

nucleR.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(nucleR)
> 
> test_check("nucleR")
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.06    0.68    7.73 

nucleR.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(nucleR)
> 
> test_check("nucleR")
== testthat results  ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   7.82    0.39    8.20 

Example timings

nucleR.Rcheck/examples_i386/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.060.010.08
coverage.rpm0.410.100.50
export.bed0.150.000.15
export.wig0.040.040.08
filterFFT0.680.040.72
fragmentLenDetect1.270.031.30
mergeCalls0.420.060.48
nucleR-package1.720.011.74
pcKeepCompDetect0.360.020.37
peakDetection1.650.021.67
peakScoring0.580.000.58
plotPeaks1.270.001.27
processReads0.390.030.42
processTilingArray000
readBAM0.140.000.19
syntheticNucMap24.72 0.0924.81

nucleR.Rcheck/examples_x64/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.070.020.08
coverage.rpm1.030.011.05
export.bed0.140.000.14
export.wig0.050.010.06
filterFFT0.950.020.97
fragmentLenDetect0.710.010.72
mergeCalls0.480.000.48
nucleR-package1.640.001.64
pcKeepCompDetect0.380.000.38
peakDetection1.890.041.92
peakScoring0.470.000.47
plotPeaks1.440.001.43
processReads0.420.000.43
processTilingArray000
readBAM0.110.000.10
syntheticNucMap29.23 0.0129.25