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CHECK report for easyRNASeq on tokay1

This page was generated on 2018-04-12 13:21:29 -0400 (Thu, 12 Apr 2018).

Package 399/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
easyRNASeq 2.14.0
Nicolas Delhomme
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/easyRNASeq
Branch: RELEASE_3_6
Last Commit: 8212b25
Last Changed Date: 2017-10-30 12:39:37 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: easyRNASeq
Version: 2.14.0
Command: rm -rf easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && mkdir easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=easyRNASeq.buildbin-libdir easyRNASeq_2.14.0.tar.gz >easyRNASeq.Rcheck\00install.out 2>&1 && cp easyRNASeq.Rcheck\00install.out easyRNASeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=easyRNASeq.buildbin-libdir --install="check:easyRNASeq-install.out" --force-multiarch --no-vignettes --timings easyRNASeq_2.14.0.tar.gz
StartedAt: 2018-04-11 23:40:48 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:47:21 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 392.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: easyRNASeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && mkdir easyRNASeq.buildbin-libdir easyRNASeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=easyRNASeq.buildbin-libdir easyRNASeq_2.14.0.tar.gz >easyRNASeq.Rcheck\00install.out 2>&1 && cp easyRNASeq.Rcheck\00install.out easyRNASeq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=easyRNASeq.buildbin-libdir --install="check:easyRNASeq-install.out" --force-multiarch --no-vignettes --timings easyRNASeq_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/easyRNASeq.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'easyRNASeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'easyRNASeq' version '2.14.0'
* 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 'easyRNASeq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:20: missing file link 'colnames'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:22: missing file link 'colnames'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:99: missing file link 'colnames'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:14: missing file link 'summarizeOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:39: missing file link 'summarizeOverlaps'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-annotation-methods.Rd:38: missing file link 'readGff3'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-package.Rd:129: missing file link 'BamFileList'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/genomeIntervals-methods.Rd:39: missing file link 'readGff3'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/parallel-methods.Rd:44: missing file link 'makePSOCKcluster'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/parallel-methods.Rd:45: missing file link 'stopCluster'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/easyRNASeq.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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.convertToUCSC'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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-3.6-bioc/meat/easyRNASeq.Rcheck/00check.log'
for details.

Installation output

easyRNASeq.Rcheck/00install.out


install for i386

* installing *source* package 'easyRNASeq' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'basename' from package 'base' in package 'easyRNASeq'
Creating a generic function for 'file.exists' from package 'base' in package 'easyRNASeq'
** help
*** installing help indices
  converting help for package 'easyRNASeq'
    finding HTML links ... done
    DESeq-methods                           html  
    finding level-2 HTML links ... done

    GenomicRanges-methods                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:20: missing file link 'colnames'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:22: missing file link 'colnames'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/GenomicRanges-methods.Rd:99: missing file link 'colnames'
    IRanges-methods                         html  
    Rsamtools-methods                       html  
    ShortRead-methods                       html  
    basename-methods                        html  
    easyRNASeq-AnnotParam-accessors         html  
    easyRNASeq-AnnotParam-class             html  
    easyRNASeq-AnnotParam                   html  
    easyRNASeq-BamFileList                  html  
    easyRNASeq-BamParam-accessors           html  
    easyRNASeq-BamParam-class               html  
    easyRNASeq-BamParam                     html  
    easyRNASeq-RnaSeqParam-accessors        html  
    easyRNASeq-RnaSeqParam-class            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:14: missing file link 'summarizeOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd:39: missing file link 'summarizeOverlaps'
    easyRNASeq-RnaSeqParam                  html  
    easyRNASeq-accessors                    html  
    easyRNASeq-annotation-internal-methods
                                            html  
    easyRNASeq-annotation-methods           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-annotation-methods.Rd:38: missing file link 'readGff3'
    easyRNASeq-class                        html  
    easyRNASeq-correction-methods           html  
    easyRNASeq-coverage-methods             html  
    easyRNASeq-datasets                     html  
    easyRNASeq-defunct-annotation-methods   html  
    easyRNASeq-defunct                      html  
    easyRNASeq-deprecated                   html  
    easyRNASeq-easyRNASeq                   html  
    easyRNASeq-global-variables             html  
    easyRNASeq-internal-AnnotParam-methods
                                            html  
    easyRNASeq-internal-methods             html  
    easyRNASeq-island-methods               html  
    easyRNASeq-package                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/easyRNASeq-package.Rd:129: missing file link 'BamFileList'
    easyRNASeq-simpleRNASeq                 html  
    easyRNASeq-summarization-internal-methods
                                            html  
    easyRNASeq-summarization-methods        html  
    easyRNASeq-synthetic-transcripts        html  
    edgeR-methods                           html  
    file.exists-methods                     html  
    genomeIntervals-methods                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/genomeIntervals-methods.Rd:39: missing file link 'readGff3'
    parallel-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/parallel-methods.Rd:44: missing file link 'makePSOCKcluster'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpqg3zBp/R.INSTALL2f2860bb7e1f/easyRNASeq/man/parallel-methods.Rd:45: missing file link 'stopCluster'
    print-methods                           html  
    show-methods                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'easyRNASeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'easyRNASeq' as easyRNASeq_2.14.0.zip
* DONE (easyRNASeq)
In R CMD INSTALL
In R CMD INSTALL

Tests output

easyRNASeq.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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.

> BiocGenerics:::testPackage("easyRNASeq")
Loading required package: GenomicRanges
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, cbind, colMeans, colSums, colnames, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
No validation performed at that stage
Validated a datasource of type biomaRt
No validation performed at that stage
Validated a datasource of type rda
Read 999 records
Validated a datasource of type gff3


RUNIT TEST PROTOCOL -- Wed Apr 11 23:46:13 2018 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
easyRNASeq RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
There were 13 warnings (use warnings() to see them)
> 
> 
> proc.time()
   user  system elapsed 
  39.62    1.39   48.35

easyRNASeq.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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.

> BiocGenerics:::testPackage("easyRNASeq")
Loading required package: GenomicRanges
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, cbind, colMeans, colSums, colnames, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
No validation performed at that stage
Validated a datasource of type biomaRt
No validation performed at that stage
Validated a datasource of type rda
Read 999 records
Validated a datasource of type gff3


RUNIT TEST PROTOCOL -- Wed Apr 11 23:47:14 2018 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
easyRNASeq RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
There were 13 warnings (use warnings() to see them)
> 
> 
> proc.time()
   user  system elapsed 
  55.01    1.25   60.64

Example timings

easyRNASeq.Rcheck/examples_i386/easyRNASeq-Ex.timings

nameusersystemelapsed
DESeq-methods000
GenomicRanges-methods0.260.040.31
IRanges-methods000
Rsamtools-methods0.040.020.75
ShortRead-methods000
easyRNASeq-AnnotParam-accessors000
easyRNASeq-AnnotParam-class000
easyRNASeq-AnnotParam000
easyRNASeq-BamFileList0.190.000.19
easyRNASeq-BamParam-accessors000
easyRNASeq-BamParam-class000
easyRNASeq-BamParam000
easyRNASeq-RnaSeqParam-accessors0.020.000.02
easyRNASeq-RnaSeqParam-class000
easyRNASeq-RnaSeqParam000
easyRNASeq-accessors000
easyRNASeq-annotation-methods000
easyRNASeq-class000
easyRNASeq-correction-methods000
easyRNASeq-coverage-methods000
easyRNASeq-easyRNASeq000
easyRNASeq-island-methods000
easyRNASeq-package000
easyRNASeq-simpleRNASeq000
easyRNASeq-summarization-methods000
easyRNASeq-synthetic-transcripts000
edgeR-methods000
genomeIntervals-methods000
parallel-methods000

easyRNASeq.Rcheck/examples_x64/easyRNASeq-Ex.timings

nameusersystemelapsed
DESeq-methods000
GenomicRanges-methods0.300.060.35
IRanges-methods000
Rsamtools-methods0.160.000.15
ShortRead-methods000
easyRNASeq-AnnotParam-accessors000
easyRNASeq-AnnotParam-class000
easyRNASeq-AnnotParam0.010.000.02
easyRNASeq-BamFileList0.170.000.17
easyRNASeq-BamParam-accessors000
easyRNASeq-BamParam-class000
easyRNASeq-BamParam0.020.000.02
easyRNASeq-RnaSeqParam-accessors000
easyRNASeq-RnaSeqParam-class000
easyRNASeq-RnaSeqParam000
easyRNASeq-accessors000
easyRNASeq-annotation-methods000
easyRNASeq-class000
easyRNASeq-correction-methods000
easyRNASeq-coverage-methods000
easyRNASeq-easyRNASeq000
easyRNASeq-island-methods000
easyRNASeq-package000
easyRNASeq-simpleRNASeq000
easyRNASeq-summarization-methods000
easyRNASeq-synthetic-transcripts000
edgeR-methods000
genomeIntervals-methods000
parallel-methods000