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CHECK report for DRIMSeq on tokay1

This page was generated on 2019-04-13 11:26:29 -0400 (Sat, 13 Apr 2019).

Package 434/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DRIMSeq 1.10.1
Malgorzata Nowicka
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DRIMSeq
Branch: RELEASE_3_8
Last Commit: 333b72b
Last Changed Date: 2019-01-04 13:30:17 -0400 (Fri, 04 Jan 2019)
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: DRIMSeq
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DRIMSeq_1.10.1.tar.gz
StartedAt: 2019-04-13 01:54:30 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:02:37 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 487.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DRIMSeq.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:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DRIMSeq_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DRIMSeq.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 'DRIMSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DRIMSeq' version '1.10.1'
* 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 'DRIMSeq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGqVEwa/R.INSTALL24ac14ba2ff0/DRIMSeq/man/dmTest.Rd:93: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGqVEwa/R.INSTALL24ac14ba2ff0/DRIMSeq/man/dmTest.Rd:193: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DRIMSeq.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 125.58   0.09  125.67
dmDStest-class     7.38   0.03    7.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 146.83   0.12  146.98
dmDStest-class     9.90   0.01    9.91
* 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/DRIMSeq.Rcheck/00check.log'
for details.



Installation output

DRIMSeq.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/DRIMSeq_1.10.1.tar.gz && rm -rf DRIMSeq.buildbin-libdir && mkdir DRIMSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DRIMSeq.buildbin-libdir DRIMSeq_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DRIMSeq_1.10.1.zip && rm DRIMSeq_1.10.1.tar.gz DRIMSeq_1.10.1.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
100 83567  100 83567    0     0  2089k      0 --:--:-- --:--:-- --:--:-- 2331k

install for i386

* installing *source* package 'DRIMSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DRIMSeq'
    finding HTML links ... done
    MatrixList-class                        html  
    dmDSdata-class                          html  
    dmDSdata                                html  
    dmDSfit-class                           html  
    dmDSprecision-class                     html  
    dmDStest-class                          html  
    dmFilter                                html  
    dmFit                                   html  
    finding level-2 HTML links ... done

    dmPrecision                             html  
    dmSQTLdata-class                        html  
    dmSQTLdata                              html  
    dmSQTLfit-class                         html  
    dmSQTLprecision-class                   html  
    dmSQTLtest-class                        html  
    dmTest                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGqVEwa/R.INSTALL24ac14ba2ff0/DRIMSeq/man/dmTest.Rd:93: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpGqVEwa/R.INSTALL24ac14ba2ff0/DRIMSeq/man/dmTest.Rd:193: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
    dm_plotDataDSInfo                       html  
    dm_plotProportions                      html  
    plotData                                html  
    plotPValues                             html  
    plotPrecision                           html  
    plotProportions                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'DRIMSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DRIMSeq' as DRIMSeq_1.10.1.zip
* DONE (DRIMSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DRIMSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

DRIMSeq.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(DRIMSeq)
> 
> test_check("DRIMSeq")
== testthat results  ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.56    0.28    5.82 

DRIMSeq.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(DRIMSeq)
> 
> test_check("DRIMSeq")
== testthat results  ===========================================================
OK: 21 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   6.92    0.18    7.10 

Example timings

DRIMSeq.Rcheck/examples_i386/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class000
dmDSdata000
dmDSfit-class0.010.000.01
dmDSprecision-class000
dmDStest-class7.380.037.41
dmFilter0.010.000.01
dmFit0.000.020.02
dmPrecision000
dmSQTLdata-class000
dmSQTLdata0.010.000.01
dmSQTLfit-class000
dmSQTLprecision-class0.020.000.02
dmSQTLtest-class125.58 0.09125.67
dmTest000
plotData000
plotPValues0.020.000.02
plotPrecision000
plotProportions000

DRIMSeq.Rcheck/examples_x64/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class000
dmDSdata000
dmDSfit-class000
dmDSprecision-class0.010.000.01
dmDStest-class9.900.019.91
dmFilter0.030.020.04
dmFit0.010.000.02
dmPrecision0.020.000.02
dmSQTLdata-class0.010.000.01
dmSQTLdata0.020.000.02
dmSQTLfit-class0.010.000.01
dmSQTLprecision-class0.020.000.02
dmSQTLtest-class146.83 0.12146.98
dmTest0.010.000.02
plotData0.020.000.01
plotPValues000
plotPrecision0.020.000.02
plotProportions000