Package: RaggedExperiment

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RaggedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RaggedExperiment_1.6.0.tar.gz

StartedAt: 2019-04-13 04:50:38 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:54:40 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 241.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RaggedExperiment.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RaggedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings RaggedExperiment_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RaggedExperiment.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 'RaggedExperiment/DESCRIPTION' ... OK
* this is package 'RaggedExperiment' version '1.6.0'
* 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 'RaggedExperiment' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:104: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:128: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:129: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:130: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:139: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:141: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:154: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:159: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:160: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:169: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:397: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:411: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/RaggedExperiment.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
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots' 'S4Vectors:::selectSome'
  See the note in ?`:::` about the use of this operator.
* 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
** running examples for arch 'x64' ... OK
* 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-3.8-bioc/meat/RaggedExperiment.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/RaggedExperiment_1.6.0.tar.gz && rm -rf RaggedExperiment.buildbin-libdir && mkdir RaggedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RaggedExperiment.buildbin-libdir RaggedExperiment_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL RaggedExperiment_1.6.0.zip && rm RaggedExperiment_1.6.0.tar.gz RaggedExperiment_1.6.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 24298  100 24298    0     0   575k      0 --:--:-- --:--:-- --:--:--  641k

install for i386

* installing *source* package 'RaggedExperiment' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RaggedExperiment'
    finding HTML links ... done
    RaggedExperiment-class                  html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:104: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:128: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:129: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:130: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:139: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:141: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:154: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:159: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:160: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:169: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:397: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpcP2W4w/R.INSTALL15482a3e832/RaggedExperiment/man/RaggedExperiment-class.Rd:411: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    RaggedExperiment-package                html  
    assay-functions                         html  
    coerce-functions                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RaggedExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RaggedExperiment' as RaggedExperiment_1.6.0.zip
* DONE (RaggedExperiment)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'RaggedExperiment' successfully unpacked and MD5 sums checked
In R CMD INSTALL

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(RaggedExperiment)
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, 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

Loading required package: S4Vectors

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: GenomeInfoDb
> 
> test_check("RaggedExperiment")
== testthat results  ===========================================================
OK: 130 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  16.70    0.54   17.25 

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(RaggedExperiment)
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, 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

Loading required package: S4Vectors

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: GenomeInfoDb
> 
> test_check("RaggedExperiment")
== testthat results  ===========================================================
OK: 130 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  14.50    0.28   14.76