Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2021-11-27 14:05:00 -0500 (Sat, 27 Nov 2021).

CHECK results for doseR on riesling1

To the developers/maintainers of the doseR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/doseR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 535/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
doseR 1.11.1  (landing page)
ake.vastermark
Snapshot Date: 2021-11-26 14:50:14 -0500 (Fri, 26 Nov 2021)
git_url: https://git.bioconductor.org/packages/doseR
git_branch: master
git_last_commit: a2e222d
git_last_commit_date: 2021-11-20 23:36:20 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: doseR
Version: 1.11.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doseR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings doseR_1.11.1.tar.gz
StartedAt: 2021-11-27 01:29:06 -0500 (Sat, 27 Nov 2021)
EndedAt: 2021-11-27 01:34:34 -0500 (Sat, 27 Nov 2021)
EllapsedTime: 328.3 seconds
RetCode: 0
Status:   OK  
CheckDir: doseR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doseR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings doseR_1.11.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/doseR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'doseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'doseR' version '1.11.1'
* package encoding: UTF-8
* 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 'doseR' 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
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running '1.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: OK


Installation output

doseR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/doseR_1.11.1.tar.gz && rm -rf doseR.buildbin-libdir && mkdir doseR.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=doseR.buildbin-libdir doseR_1.11.1.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL doseR_1.11.1.zip && rm doseR_1.11.1.tar.gz doseR_1.11.1.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
  6  617k    6 40527    0     0   262k      0  0:00:02 --:--:--  0:00:02  260k
100  617k  100  617k    0     0  2063k      0 --:--:-- --:--:-- --:--:-- 2063k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'doseR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'doseR'
    finding HTML links ... done
    dafs                                    html  
    dafsFilter                              html  
    generateStats                           html  
    getLibsizes3                            html  
    glSeq                                   html  
    hmel.dat                                html  
    iqrxFilter                              html  
    make_RPKM                               html  
    plotExpr                                html  
    plotMA.se                               html  
    plotRatioBoxes                          html  
    plotRatioDensity                        html  
    quantFilter                             html  
    se.DM                                   html  
    se                                      html  
    simpleFilter                            html  
    test_diffs                              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
* MD5 sums
packaged installation of 'doseR' as doseR_1.11.1.zip
* DONE (doseR)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'doseR' successfully unpacked and MD5 sums checked

Tests output

doseR.Rcheck/tests/1.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(doseR)
> 
> data(hmel.se)
> f_se <- quantFilter(se, lo.bound = 0.4, hi.bound = 0.5)
Filtering removed 12660 (92.96%) of 13619 total loci.
> dm <- se.DM(f_se)
> temp <- glSeq(dm, "-1 + replicate")
> 
> RUnit::checkEqualsNumeric(round(temp@optinfo$val[4], 1), round(6.008, 1))
[1] TRUE
> RUnit::checkEqualsNumeric(round(temp@optinfo$val[5], 1), round(5.840, 1))
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   6.90    0.20    7.09 

Example timings

doseR.Rcheck/doseR-Ex.timings

nameusersystemelapsed
dafs1.950.272.22
dafsFilter1.550.061.61
generateStats0.090.000.09
getLibsizes30.060.000.06
glSeq3.020.053.06
iqrxFilter0.060.010.08
make_RPKM0.080.000.08
plotExpr0.090.000.09
plotMA.se0.170.020.19
plotRatioBoxes0.250.000.25
plotRatioDensity0.080.020.10
quantFilter0.060.000.06
se.DM0.130.030.15
simpleFilter0.160.000.16
test_diffs0.100.000.11