Michael Lawrence
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/HelloRanges |
| Branch: RELEASE_3_11 |
| Last Commit: 39dafc4 |
| Last Changed Date: 2020-04-27 15:02:58 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:49 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE HelloRanges PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 809/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HelloRanges 1.14.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: HelloRanges |
| Version: 1.14.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HelloRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings HelloRanges_1.14.0.tar.gz |
| StartedAt: 2020-10-17 04:54:02 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:08:11 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 849.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HelloRanges.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HelloRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings HelloRanges_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/HelloRanges.Rcheck' * using R version 4.0.3 (2020-10-10) * 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 '1.14.0' * 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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/HelloRanges/man/bedtools_shift.Rd:76: file link 'shift' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-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 ... 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 '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: 1 WARNING, 2 NOTEs See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/HelloRanges.Rcheck/00check.log' for details.
HelloRanges.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/HelloRanges_1.14.0.tar.gz && rm -rf HelloRanges.buildbin-libdir && mkdir HelloRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HelloRanges.buildbin-libdir HelloRanges_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL HelloRanges_1.14.0.zip && rm HelloRanges_1.14.0.tar.gz HelloRanges_1.14.0.zip
###
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% 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 1132k 100 1132k 0 0 14.7M 0 --:--:-- --:--:-- --:--:-- 16.2M
install for i386
* installing *source* package 'HelloRanges' ...
** using staged installation
** 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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/HelloRanges/man/bedtools_shift.Rd:76: file link 'shift' in package 'IRanges' does not exist and so has been treated as a topic
bedtools_slop html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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-3.11-bioc/tmpdir/RtmpYL26qD/R.INSTALL2c5027075712/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 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 'HelloRanges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HelloRanges' as HelloRanges_1.14.0.zip
* DONE (HelloRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'HelloRanges' successfully unpacked and MD5 sums checked
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HelloRanges.Rcheck/tests_i386/HelloRanges_unit_tests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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
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
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
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 -- Sat Oct 17 05:06:31 2020
***********************************************
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
44.09 1.56 54.15
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HelloRanges.Rcheck/tests_x64/HelloRanges_unit_tests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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
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
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
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 -- Sat Oct 17 05:07:26 2020
***********************************************
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
46.73 0.54 52.39
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HelloRanges.Rcheck/examples_i386/HelloRanges-Ex.timings
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HelloRanges.Rcheck/examples_x64/HelloRanges-Ex.timings
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