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CHECK report for RNAprobR on tokay1

This page was generated on 2021-05-06 12:33:19 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RNAprobR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1553/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAprobR 1.22.0  (landing page)
Nikos Sidiropoulos
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RNAprobR
Branch: RELEASE_3_12
Last Commit: a1d0885
Last Changed Date: 2020-10-27 11:03:22 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RNAprobR
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAprobR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RNAprobR_1.22.0.tar.gz
StartedAt: 2021-05-06 06:21:31 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:27:35 -0400 (Thu, 06 May 2021)
EllapsedTime: 364.3 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: RNAprobR.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RNAprobR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RNAprobR_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RNAprobR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAprobR/DESCRIPTION' ... OK
* this is package 'RNAprobR' version '1.22.0'
* 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 'RNAprobR' can be installed ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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-3.12-bioc/meat/RNAprobR.Rcheck/00check.log'
for details.



Installation output

RNAprobR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/RNAprobR_1.22.0.tar.gz && rm -rf RNAprobR.buildbin-libdir && mkdir RNAprobR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RNAprobR.buildbin-libdir RNAprobR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RNAprobR_1.22.0.zip && rm RNAprobR_1.22.0.tar.gz RNAprobR_1.22.0.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  331k  100  331k    0     0  20.7M      0 --:--:-- --:--:-- --:--:-- 23.1M

install for i386

* installing *source* package 'RNAprobR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RNAprobR'
    finding HTML links ... done
    BED2txDb                                html  
    GR2norm_df                              html  
    bam2bedgraph                            html  
    bedgraph2norm                           html  
    comp                                    html  
    compdata                                html  
    correct_oversaturation                  html  
    dtcr                                    html  
    k2n_calc                                html  
    norm2bedgraph                           html  
    norm_df2GR                              html  
    plotRNA                                 html  
    plotReads                               html  
    readsamples                             html  
    slograt                                 html  
    swinsor                                 html  
    swinsor_vector                          html  
    winsor                                  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 'RNAprobR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNAprobR' as RNAprobR_1.22.0.zip
* DONE (RNAprobR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RNAprobR' successfully unpacked and MD5 sums checked

Tests output


Example timings

RNAprobR.Rcheck/examples_i386/RNAprobR-Ex.timings

nameusersystemelapsed
BED2txDb0.620.220.84
GR2norm_df0.330.000.33
bedgraph2norm2.070.362.44
comp0.150.000.16
compdata0.240.030.26
correct_oversaturation0.110.000.11
dtcr0.320.000.33
k2n_calc0.020.000.02
norm2bedgraph0.690.000.68
norm_df2GR0.010.000.02
plotRNA0.250.080.33
plotReads0.140.000.14
readsamples0.020.000.01
slograt0.410.000.41
swinsor0.340.000.34
swinsor_vector0.050.000.05
winsor0.010.000.02

RNAprobR.Rcheck/examples_x64/RNAprobR-Ex.timings

nameusersystemelapsed
BED2txDb1.560.021.57
GR2norm_df0.340.000.35
bedgraph2norm1.980.022.00
comp0.180.000.17
compdata0.260.000.27
correct_oversaturation0.110.000.11
dtcr0.610.010.62
k2n_calc0.010.000.02
norm2bedgraph1.350.001.34
norm_df2GR0.040.000.05
plotRNA0.390.000.39
plotReads0.240.000.23
readsamples0.040.000.05
slograt0.680.000.67
swinsor0.400.000.41
swinsor_vector0.060.000.06
winsor0.020.000.01