Multiple platform build/check report for BioC 3.7 - CHECK report for HelloRanges on tokay2

Package: HelloRanges

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HelloRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings HelloRanges_1.6.0.tar.gz

StartedAt: 2018-10-17 02:40:17 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:47:20 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 423.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: HelloRanges.Rcheck

Warnings: 2

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HelloRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings HelloRanges_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/HelloRanges.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 'HelloRanges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HelloRanges' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomicRanges' 'Biostrings'
  'BSgenome' 'GenomicFeatures' 'VariantAnnotation' 'Rsamtools'
  'GenomicAlignments' 'rtracklayer' 'GenomeInfoDb'
  'SummarizedExperiment'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'HelloRanges' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:126: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:150: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:150: file link 'precede' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:151: file link 'follow' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:151: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_complement.Rd:59: file link 'setdiff' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_complement.Rd:62: file link 'gaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_coverage.Rd:127: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_flank.Rd:83: file link 'flank' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_genomecov.Rd:112: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_getfasta.Rd:72: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_getfasta.Rd:76: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_groupby.Rd:77: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_jaccard.Rd:97: file link 'intersect' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_jaccard.Rd:98: file link 'union' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_makewindows.Rd:71: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_makewindows.Rd:72: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_map.Rd:123: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_map.Rd:124: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_map.Rd:125: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_merge.Rd:89: file link 'reduce' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_merge.Rd:91: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_merge.Rd:111: file link 'reduce' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_multiinter.Rd:10: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_multiinter.Rd:69: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_multiinter.Rd:87: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_nuc.Rd:69: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_nuc.Rd:71: file link 'vcountPattern' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_shift.Rd:76: missing file link 'shift'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_slop.Rd:83: file link 'resize' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_subtract.Rd:107: file link 'setdiff' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_subtract.Rd:118: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_unionbedg.Rd:10: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_unionbedg.Rd:85: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/pair.Rd:45: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/HelloRanges.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
Packages in Depends field not imported from:
  'BSgenome' 'GenomicAlignments' 'GenomicFeatures' 'VariantAnnotation'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'IRanges:::subgrouping'
  'S4Vectors:::make_zero_col_DataFrame'
  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 ... WARNING
Missing link or links in documentation object 'bedtools_shift.Rd':
  '[GenomicRanges]{shift}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 'HelloRanges_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'HelloRanges_unit_tests.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: 2 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/HelloRanges.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/HelloRanges_1.6.0.tar.gz && rm -rf HelloRanges.buildbin-libdir && mkdir HelloRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HelloRanges.buildbin-libdir HelloRanges_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL HelloRanges_1.6.0.zip && rm HelloRanges_1.6.0.tar.gz HelloRanges_1.6.0.zip
###
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100 1132k  100 1132k    0     0  18.2M      0 --:--:-- --:--:-- --:--:-- 20.4M

install for i386

* installing *source* package 'HelloRanges' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HelloRanges'
    finding HTML links ... done
    argparse                                html  
    bedtools_closest                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:126: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:150: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:150: file link 'precede' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:151: file link 'follow' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_closest.Rd:151: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_complement                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_complement.Rd:59: file link 'setdiff' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_complement.Rd:62: file link 'gaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_coverage                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_coverage.Rd:127: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_flank                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_flank.Rd:83: file link 'flank' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_genomecov                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_genomecov.Rd:112: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_getfasta                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_getfasta.Rd:72: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_getfasta.Rd:76: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    bedtools_groupby                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_groupby.Rd:77: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
    bedtools_intersect                      html  
    bedtools_jaccard                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_jaccard.Rd:97: file link 'intersect' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_jaccard.Rd:98: file link 'union' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_makewindows                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_makewindows.Rd:71: file link 'tile' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_makewindows.Rd:72: file link 'slidingWindows' in package 'IRanges' does not exist and so has been treated as a topic
    bedtools_map                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_map.Rd:123: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_map.Rd:124: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_map.Rd:125: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
    bedtools_merge                          html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_merge.Rd:89: file link 'reduce' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_merge.Rd:91: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_merge.Rd:111: file link 'reduce' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_multiinter                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_multiinter.Rd:10: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_multiinter.Rd:69: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_multiinter.Rd:87: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_nuc                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_nuc.Rd:69: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_nuc.Rd:71: file link 'vcountPattern' in package 'Biostrings' does not exist and so has been treated as a topic
    bedtools_shift                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_shift.Rd:76: missing file link 'shift'
    bedtools_slop                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_slop.Rd:83: file link 'resize' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_subtract                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_subtract.Rd:107: file link 'setdiff' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_subtract.Rd:118: file link 'subsetByOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
    bedtools_unionbedg                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_unionbedg.Rd:10: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/bedtools_unionbedg.Rd:85: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
    distmode                                html  
    pair                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpuGfJnW/R.INSTALL1ba0166928cc/HelloRanges/man/pair.Rd:45: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'HelloRanges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HelloRanges' as HelloRanges_1.6.0.zip
* DONE (HelloRanges)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'HelloRanges' successfully unpacked and MD5 sums checked
In R CMD INSTALL


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.

> require("HelloRanges") || stop("unable to load HelloRanges package")
Loading required package: HelloRanges
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
Loading required package: stats4

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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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: VariantAnnotation
Loading required package: SummarizedExperiment
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 object is masked from 'package:Biostrings':

    type

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

    aperm, apply

Loading required package: Rsamtools

Attaching package: 'VariantAnnotation'

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

    tabulate

Loading required package: GenomicAlignments
[1] TRUE
> HelloRanges:::.test()


RUNIT TEST PROTOCOL -- Wed Oct 17 02:46:22 2018 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HelloRanges RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  44.39    1.46   50.93 
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.


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.

> require("HelloRanges") || stop("unable to load HelloRanges package")
Loading required package: HelloRanges
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
Loading required package: stats4

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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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: VariantAnnotation
Loading required package: SummarizedExperiment
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 object is masked from 'package:Biostrings':

    type

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

    aperm, apply

Loading required package: Rsamtools

Attaching package: 'VariantAnnotation'

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

    tabulate

Loading required package: GenomicAlignments
[1] TRUE
> HelloRanges:::.test()


RUNIT TEST PROTOCOL -- Wed Oct 17 02:47:11 2018 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HelloRanges RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  47.53    0.76   48.28 
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.

name	user	system	elapsed
bedtools_closest	0.43	0.14	0.58
bedtools_complement	0.03	0.02	0.04
bedtools_coverage	0.22	0.03	0.25
bedtools_flank	0.09	0.00	0.09
bedtools_genomecov	0.11	0.00	0.11
bedtools_getfasta	0.05	0.00	0.05
bedtools_groupby	0.05	0.00	0.04
bedtools_intersect	0.36	0.00	0.36
bedtools_jaccard	0.09	0.00	0.10
bedtools_makewindows	0.09	0.00	0.09
bedtools_map	0.25	0.00	0.25
bedtools_merge	0.25	0.00	0.25
bedtools_multiinter	0.09	0.00	0.10
bedtools_nuc	0.08	0.00	0.08
bedtools_shift	0.09	0.00	0.09
bedtools_slop	0.08	0.00	0.08
bedtools_subtract	0.15	0.00	0.16
bedtools_unionbedg	0.07	0.00	0.06
distmode	0	0	0

name	user	system	elapsed
bedtools_closest	0.36	0.03	0.39
bedtools_complement	0.02	0.00	0.01
bedtools_coverage	0.16	0.02	0.17
bedtools_flank	0.16	0.00	0.16
bedtools_genomecov	0.23	0.01	0.25
bedtools_getfasta	0.06	0.00	0.06
bedtools_groupby	0.08	0.00	0.08
bedtools_intersect	0.5	0.0	0.5
bedtools_jaccard	0.09	0.00	0.10
bedtools_makewindows	0.09	0.00	0.09
bedtools_map	0.19	0.00	0.19
bedtools_merge	0.38	0.02	0.39
bedtools_multiinter	0.08	0.00	0.08
bedtools_nuc	0.04	0.00	0.04
bedtools_shift	0.06	0.00	0.07
bedtools_slop	0.07	0.00	0.06
bedtools_subtract	0.11	0.00	0.11
bedtools_unionbedg	0.06	0.00	0.06
distmode	0	0	0

CHECK report for HelloRanges on tokay2

Summary

Command output

Installation output

Tests output

Example timings