Michael Lawrence
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/HelloRanges |
| Branch: master |
| Last Commit: 2e0da74 |
| Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:27:53 -0400 (Tue, 09 Apr 2019).
| Package 736/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HelloRanges 1.9.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: HelloRanges |
| Version: 1.9.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HelloRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HelloRanges_1.9.0.tar.gz |
| StartedAt: 2019-04-09 03:26:26 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:35:01 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 515.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: HelloRanges.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HelloRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings HelloRanges_1.9.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/HelloRanges.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.9.0'
* 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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-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'
ERROR
Running the tests in 'tests/HelloRanges_unit_tests.R' failed.
Last 13 lines of output:
HelloRanges RUnit Tests - 17 test functions, 1 error, 0 failures
ERROR in test_merge: Error in validObject(.Object) :
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Test files with failing tests
test_merge.R
test_merge
Error in BiocGenerics:::testPackage("HelloRanges") :
unit tests failed for package HelloRanges
Calls: <Anonymous> -> <Anonymous>
Execution halted
** running tests for arch 'x64' ...
Running 'HelloRanges_unit_tests.R'
ERROR
Running the tests in 'tests/HelloRanges_unit_tests.R' failed.
Last 13 lines of output:
HelloRanges RUnit Tests - 17 test functions, 1 error, 0 failures
ERROR in test_merge: Error in validObject(.Object) :
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Test files with failing tests
test_merge.R
test_merge
Error in BiocGenerics:::testPackage("HelloRanges") :
unit tests failed for package HelloRanges
Calls: <Anonymous> -> <Anonymous>
Execution halted
* 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 ERRORs, 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-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/3.9/bioc/src/contrib/HelloRanges_1.9.0.tar.gz && rm -rf HelloRanges.buildbin-libdir && mkdir HelloRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HelloRanges.buildbin-libdir HelloRanges_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL HelloRanges_1.9.0.zip && rm HelloRanges_1.9.0.tar.gz HelloRanges_1.9.0.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 13.9M 0 --:--:-- --:--:-- --:--:-- 15.3M
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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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-3.9-bioc/tmpdir/RtmpSkKV8u/R.INSTALL1e30b7a2791/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_1.9.0.zip
* DONE (HelloRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'HelloRanges' successfully unpacked and MD5 sums checked
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HelloRanges.Rcheck/tests_i386/HelloRanges_unit_tests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.
> 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, 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, 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()
Timing stopped at: 1.39 0 5.7
Error in validObject(.Object) :
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
RUNIT TEST PROTOCOL -- Tue Apr 09 03:33:10 2019
***********************************************
Number of test functions: 17
Number of errors: 1
Number of failures: 0
1 Test Suite :
HelloRanges RUnit Tests - 17 test functions, 1 error, 0 failures
ERROR in test_merge: Error in validObject(.Object) :
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Test files with failing tests
test_merge.R
test_merge
Error in BiocGenerics:::testPackage("HelloRanges") :
unit tests failed for package HelloRanges
Calls: <Anonymous> -> <Anonymous>
Execution halted
|
HelloRanges.Rcheck/tests_x64/HelloRanges_unit_tests.Rout.fail
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.
> 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, 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, 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()
Timing stopped at: 1.34 0 1.34
Error in validObject(.Object) :
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
RUNIT TEST PROTOCOL -- Tue Apr 09 03:34:14 2019
***********************************************
Number of test functions: 17
Number of errors: 1
Number of failures: 0
1 Test Suite :
HelloRanges RUnit Tests - 17 test functions, 1 error, 0 failures
ERROR in test_merge: Error in validObject(.Object) :
invalid class "VCFHeader" object: 1: 'info(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
invalid class "VCFHeader" object: 2: 'geno(VCFHeader)' must be a 3 column DataFrame with names Number, Type, Description
Test files with failing tests
test_merge.R
test_merge
Error in BiocGenerics:::testPackage("HelloRanges") :
unit tests failed for package HelloRanges
Calls: <Anonymous> -> <Anonymous>
Execution halted
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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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