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CHECK report for DChIPRep on tokay2

This page was generated on 2019-10-16 12:34:19 -0400 (Wed, 16 Oct 2019).

Package 393/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DChIPRep 1.14.0
Bernd Klaus
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/DChIPRep
Branch: RELEASE_3_9
Last Commit: e296b91
Last Changed Date: 2019-05-02 11:53:58 -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: DChIPRep
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DChIPRep.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DChIPRep_1.14.0.tar.gz
StartedAt: 2019-10-16 03:04:43 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:15:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 640.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DChIPRep.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DChIPRep.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DChIPRep_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DChIPRep.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 'DChIPRep/DESCRIPTION' ... OK
* this is package 'DChIPRep' version '1.14.0'
* 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 'DChIPRep' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:36: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:14: file link 'GenomicRanges-class' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:27: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:65: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/robust_mean.Rd:17: file link 'smhuber' in package 'smoothmest' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DChIPRep.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
importData                 7.94   0.03    8.22
plotProfiles               6.10   0.20    6.29
plotSignificance           6.09   0.08    6.17
FDRresults                 3.98   1.08    5.06
show                       3.53   0.02    8.14
summarizeCountsPerPosition 2.66   0.01    5.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotSignificance 6.86   0.04    6.90
plotProfiles     6.55   0.10    6.64
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/DChIPRep.Rcheck/00check.log'
for details.



Installation output

DChIPRep.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DChIPRep_1.14.0.tar.gz && rm -rf DChIPRep.buildbin-libdir && mkdir DChIPRep.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DChIPRep.buildbin-libdir DChIPRep_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DChIPRep_1.14.0.zip && rm DChIPRep_1.14.0.tar.gz DChIPRep_1.14.0.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
100  690k  100  690k    0     0  9104k      0 --:--:-- --:--:-- --:--:--  9.7M

install for i386

* installing *source* package 'DChIPRep' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB

** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DChIPRep'
    finding HTML links ... done
    DChIPRep                                html  
    DChIPRepResults                         html  
    DESeq2Data                              html  
    FDRresults                              html  
    TSS_galonska                            html  
    chip_galonska                           html  
    exampleChipData                         html  
    exampleInputData                        html  
    exampleSampleTable                      html  
    getMATfromDataFrame                     html  
    importData                              html  
    importDataFromMatrices                  html  
    importData_soGGi                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:36: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:14: file link 'GenomicRanges-class' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:27: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/importData_soGGi.Rd:65: file link 'regionPlot' in package 'soGGi' does not exist and so has been treated as a topic
    input_galonska                          html  
    plotProfiles                            html  
    plotSignificance                        html  
    resultsDChIPRep                         html  
    robust_mean                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmp6HUW2O/R.INSTALL1dd03b55140c/DChIPRep/man/robust_mean.Rd:17: file link 'smhuber' in package 'smoothmest' does not exist and so has been treated as a topic
    runTesting                              html  
    sample_table_galonska                   html  
    show                                    html  
    summarizeCountsPerPosition              html  
    testData                                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 'DChIPRep' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DChIPRep' as DChIPRep_1.14.0.zip
* DONE (DChIPRep)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DChIPRep' successfully unpacked and MD5 sums checked

Tests output

DChIPRep.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(DChIPRep)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum


> 
> test_check("DChIPRep")
Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

== testthat results  ===========================================================
[ OK: 19 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> 
> # code for checking and saving the log
> ## ff <- file("check.out", open = "wt")
> ## sink(file = ff, type = "message")
> ##  sink(type = "message")
>  ##    sink() 
> 
> 
> 
> proc.time()
   user  system elapsed 
  33.23    2.03   35.32 

DChIPRep.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(DChIPRep)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum


> 
> test_check("DChIPRep")
Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

== testthat results  ===========================================================
[ OK: 19 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> 
> # code for checking and saving the log
> ## ff <- file("check.out", open = "wt")
> ## sink(file = ff, type = "message")
> ##  sink(type = "message")
>  ##    sink() 
> 
> 
> 
> proc.time()
   user  system elapsed 
  33.12    0.78   33.89 

Example timings

DChIPRep.Rcheck/examples_i386/DChIPRep-Ex.timings

nameusersystemelapsed
DChIPRepResults0.160.040.20
DESeq2Data0.050.100.14
FDRresults3.981.085.06
getMATfromDataFrame2.750.053.13
importData7.940.038.22
importDataFromMatrices0.260.030.30
importData_soGGi000
plotProfiles6.100.206.29
plotSignificance6.090.086.17
resultsDChIPRep3.520.003.52
robust_mean0.060.000.06
runTesting2.860.003.64
show3.530.028.14
summarizeCountsPerPosition2.660.015.48

DChIPRep.Rcheck/examples_x64/DChIPRep-Ex.timings

nameusersystemelapsed
DChIPRepResults0.070.040.09
DESeq2Data0.070.000.08
FDRresults3.960.144.09
getMATfromDataFrame2.730.002.74
importData4.960.034.98
importDataFromMatrices0.320.010.35
importData_soGGi000
plotProfiles6.550.106.64
plotSignificance6.860.046.90
resultsDChIPRep3.670.003.68
robust_mean0.050.000.04
runTesting3.780.023.80
show3.970.034.00
summarizeCountsPerPosition1.800.021.81