Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

CHECK report for nucleR on tokay2

This page was generated on 2019-10-16 12:25:26 -0400 (Wed, 16 Oct 2019).

Package 1116/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 2.16.0
Diego Gallego
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/nucleR
Branch: RELEASE_3_9
Last Commit: e5c0efe
Last Changed Date: 2019-05-02 11:53:27 -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: nucleR
Version: 2.16.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nucleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings nucleR_2.16.0.tar.gz
StartedAt: 2019-10-16 05:38:21 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:44:13 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 352.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: nucleR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:nucleR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings nucleR_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/nucleR.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 'nucleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'nucleR' version '2.16.0'
* 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 'nucleR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-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 30.25   0.11   30.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
syntheticNucMap 32.65   0.05   32.71
* 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/nucleR.Rcheck/00check.log'
for details.



Installation output

nucleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/nucleR_2.16.0.tar.gz && rm -rf nucleR.buildbin-libdir && mkdir nucleR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=nucleR.buildbin-libdir nucleR_2.16.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL nucleR_2.16.0.zip && rm nucleR_2.16.0.tar.gz nucleR_2.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  805k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  805k  100  805k    0     0  11.9M      0 --:--:-- --:--:-- --:--:-- 13.1M

install for i386

* installing *source* package 'nucleR' ...
** using staged installation
** 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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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-3.9-bioc/tmpdir/RtmpaCSIWz/R.INSTALL204852a0359c/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 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 'nucleR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'nucleR' as nucleR_2.16.0.zip
* DONE (nucleR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'nucleR' successfully unpacked and MD5 sums checked

Tests output

nucleR.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(nucleR)
> 
> test_check("nucleR")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   9.79    0.65   10.43 

nucleR.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(nucleR)
> 
> test_check("nucleR")
== testthat results  ===========================================================
[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.84    0.43    9.26 

Example timings

nucleR.Rcheck/examples_i386/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.110.010.12
coverage.rpm0.490.100.58
export.bed0.140.000.14
export.wig0.050.010.06
filterFFT0.890.030.92
fragmentLenDetect0.980.011.00
mergeCalls0.440.000.43
nucleR-package2.00.12.1
pcKeepCompDetect0.390.010.40
peakDetection1.460.221.69
peakScoring0.400.030.44
plotPeaks1.080.021.09
processReads0.390.050.44
processTilingArray000
readBAM0.230.000.47
syntheticNucMap30.25 0.1130.36

nucleR.Rcheck/examples_x64/nucleR-Ex.timings

nameusersystemelapsed
controlCorrection0.060.000.06
coverage.rpm0.980.011.00
export.bed0.140.020.16
export.wig0.140.010.15
filterFFT0.910.000.91
fragmentLenDetect0.50.00.5
mergeCalls0.510.000.53
nucleR-package1.720.021.73
pcKeepCompDetect0.380.010.40
peakDetection1.510.031.54
peakScoring0.470.000.47
plotPeaks1.220.001.22
processReads0.530.020.55
processTilingArray000
readBAM0.190.000.18
syntheticNucMap32.65 0.0532.71