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CHECK report for biobroom on tokay2

This page was generated on 2018-10-17 08:41:19 -0400 (Wed, 17 Oct 2018).

Package 123/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biobroom 1.12.1
John D. Storey and Andrew J. Bass
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/biobroom
Branch: RELEASE_3_7
Last Commit: 5a2a7a8
Last Changed Date: 2018-08-09 12:15:21 -0400 (Thu, 09 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biobroom
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biobroom.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings biobroom_1.12.1.tar.gz
StartedAt: 2018-10-17 00:42:51 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:45:00 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 128.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: biobroom.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biobroom.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings biobroom_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/biobroom.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biobroom/DESCRIPTION' ... OK
* this is package 'biobroom' version '1.12.1'
* 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 'biobroom' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw9nvBX/R.INSTALL6b8244b67b7/biobroom/man/ExpressionSet_tidiers.Rd:17: file link 'assayDataElement' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/biobroom.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 ... NOTE
'library' or 'require' call to 'DESeq2' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'dplyr::tbl_dt'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
finish: no visible global function definition for 'tbl_dt'
glance.DGEExact: no visible global function definition for 'p.adjust'
glance.GRanges: no visible binding for global variable 'gr'
glance.GRangesList: no visible binding for global variable 'gr'
makeExampleDataSet: no visible global function definition for
  'estimateSizeFactors'
makeExampleDataSet: no visible global function definition for 'counts'
makeExampleDataSet: no visible global function definition for 'colData'
makeExampleDataSet: no visible global function definition for
  'seqnames'
makeExampleDataSet: no visible global function definition for
  'rowRanges'
makeExampleDataSet: no visible global function definition for 'start'
makeExampleDataSet: no visible global function definition for 'end'
makeExampleDataSet: no visible global function definition for 'DGEList'
makeExampleDataSet: no visible global function definition for
  'calcNormFactors'
makeExampleDataSet: no visible global function definition for
  'model.matrix'
makeExampleDataSet: no visible global function definition for 'design'
makeExampleDataSet: no visible global function definition for
  'voomWithQualityWeights'
makeExampleDataSet: no visible global function definition for 'voom'
makeExampleDataSet: no visible global function definition for 'pData<-'
makeExampleDataSet: no visible global function definition for 'fData<-'
makeExampleDataSet: no visible global function definition for 'is'
tidy.DESeqDataSet: no visible binding for global variable 'term'
tidy.DESeqDataSet: no visible binding for global variable '.'
tidy.DESeqDataSet: no visible global function definition for 'counts'
tidy.DESeqDataSet: no visible binding for global variable 'gene'
tidy.DGEList: no visible binding for global variable 'gene'
tidy.EList: no visible global function definition for 'setNames'
tidy.ExpressionSet: no visible binding for global variable 'value'
tidy.ExpressionSet: no visible binding for global variable 'gene'
tidy.ExpressionSet: no visible global function definition for 'pData'
tidy.MArrayLM: no visible binding for global variable 'term'
tidy.MArrayLM: no visible binding for global variable 'estimate'
tidy.MArrayLM: no visible binding for global variable 'gene'
tidy.MSnSet: no visible binding for global variable 'sample.id'
tidy.MSnSet: no visible binding for global variable 'value'
tidy.MSnSet: no visible binding for global variable 'protein'
tidy.MSnSet: no visible global function definition for 'pData'
tidy.RangedSummarizedExperiment: no visible binding for global variable
  'value'
tidy.RangedSummarizedExperiment: no visible binding for global variable
  'gene'
tidy.RangedSummarizedExperiment: no visible global function definition
  for 'colData'
tidy.deSet: no visible global function definition for 'exprs<-'
tidy.deSet: no visible binding for global variable 'value'
tidy.deSet: no visible binding for global variable 'gene'
tidy.deSet: no visible global function definition for 'pData'
tidy.qvalue: no visible binding for global variable 'smoothed'
tidy.qvalue: no visible binding for global variable 'pi0'
tidy.qvalue: no visible binding for global variable 'lambda'
tidy_matrix: no visible binding for global variable 'value'
tidy_matrix: no visible binding for global variable 'gene'
Undefined global functions or variables:
  . DGEList calcNormFactors colData counts design end estimate
  estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix
  p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames
  setNames smoothed start tbl_dt term value voom voomWithQualityWeights
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "end", "model.matrix", "p.adjust", "setNames",
             "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
DESeq2_tidiers 9.37   0.55    9.96
edgeR_tidiers  5.56   0.19    5.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
DESeq2_tidiers 8.75   0.32    9.08
edgeR_tidiers  5.83   0.09    5.93
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/biobroom.Rcheck/00check.log'
for details.



Installation output

biobroom.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/biobroom_1.12.1.tar.gz && rm -rf biobroom.buildbin-libdir && mkdir biobroom.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biobroom.buildbin-libdir biobroom_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL biobroom_1.12.1.zip && rm biobroom_1.12.1.tar.gz biobroom_1.12.1.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  218k  100  218k    0     0  3599k      0 --:--:-- --:--:-- --:--:-- 4050k

install for i386

* installing *source* package 'biobroom' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biobroom'
    finding HTML links ... done
    DESeq2_tidiers                          html  
    ExpressionSet_tidiers                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmpw9nvBX/R.INSTALL6b8244b67b7/biobroom/man/ExpressionSet_tidiers.Rd:17: file link 'assayDataElement' in package 'Biobase' does not exist and so has been treated as a topic
    GRanges_tidiers                         html  
    MSnSet_tidiers                          html  
    SummarizedExperiment_tidiers            html  
    biobroom                                html  
    edgeR_tidiers                           html  
    edge_tidiers                            html  
    hammer                                  html  
    limma_tidiers                           html  
    list_tidiers                            html  
    qvalue_tidiers                          html  
    sva_tidiers                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'biobroom' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biobroom' as biobroom_1.12.1.zip
* DONE (biobroom)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'biobroom' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

biobroom.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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("magrittr")

Attaching package: 'magrittr'

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

    equals, is_less_than, not

> library("dplyr")

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library("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:dplyr':

    combine, intersect, setdiff, union

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    first, rename

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

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

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

    count

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

> library("edgeR")
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

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

    plotMA

> library("Biobase")
> library("biobroom")
Loading required package: broom
> 
> test_check("biobroom")
== testthat results  ===========================================================
OK: 52 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
  11.70    0.82   12.51 

biobroom.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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("magrittr")

Attaching package: 'magrittr'

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

    equals, is_less_than, not

> library("dplyr")

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library("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:dplyr':

    combine, intersect, setdiff, union

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    first, rename

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

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

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

    count

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

> library("edgeR")
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

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

    plotMA

> library("Biobase")
> library("biobroom")
Loading required package: broom
> 
> test_check("biobroom")
== testthat results  ===========================================================
OK: 52 SKIPPED: 0 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
  13.65    0.43   14.09 

Example timings

biobroom.Rcheck/examples_i386/biobroom-Ex.timings

nameusersystemelapsed
DESeq2_tidiers9.370.559.96
ExpressionSet_tidiers1.20.01.2
GRanges_tidiers000
MSnSet_tidiers1.940.392.50
SummarizedExperiment_tidiers000
edgeR_tidiers5.560.195.75
limma_tidiers0.380.000.37
qvalue_tidiers0.720.000.72

biobroom.Rcheck/examples_x64/biobroom-Ex.timings

nameusersystemelapsed
DESeq2_tidiers8.750.329.08
ExpressionSet_tidiers1.350.041.39
GRanges_tidiers000
MSnSet_tidiers2.000.072.25
SummarizedExperiment_tidiers000
edgeR_tidiers5.830.095.93
limma_tidiers0.370.000.37
qvalue_tidiers0.630.030.66