Bioconductor Package Maintainer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GenomicFiles |
| Branch: master |
| Last Commit: bcfcb6e |
| Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:18:57 -0400 (Tue, 09 Apr 2019).
| Package 648/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GenomicFiles 1.19.0 Bioconductor Package Maintainer
| 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: GenomicFiles |
| Version: 1.19.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomicFiles_1.19.0.tar.gz |
| StartedAt: 2019-04-09 03:00:24 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:16:23 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 959.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicFiles.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:GenomicFiles.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GenomicFiles_1.19.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicFiles.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 'GenomicFiles/DESCRIPTION' ... OK
* this is package 'GenomicFiles' version '1.19.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'GenomicRanges', 'SummarizedExperiment',
'BiocParallel', 'Rsamtools', 'rtracklayer'
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 'GenomicFiles' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/GenomicFiles-class.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:78: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:129: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:130: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:133: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:139: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:143: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:148: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:162: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:170: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:180: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/reduceByYield.Rd:12: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/reduceByYield.Rd:29: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/reduceByYield.Rd:121: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/reduceByYield.Rd:122: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicFiles.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 ... OK
* 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' ... ERROR
Running examples in 'GenomicFiles-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VcfStack
> ### Title: VcfStack and RangedVcfStack Objects
> ### Aliases: class:VcfStack VcfStack-class RangedVcfStack-class VcfStack
> ### RangedVcfStack colnames,VcfStack-method rownames,VcfStack-method
> ### dimnames,VcfStack-method files,VcfStack-method
> ### files<-,VcfStack,character-method files<-,VcfStack,VcfFile-method
> ### files<-,VcfStack,VcfFileList-method seqinfo,VcfStack-method
> ### seqinfo<-,VcfStack-method seqinfo<-,RangedVcfStack-method
> ### seqlevelsStyle<-,VcfStack-method
> ### seqlevelsStyle<-,RangedVcfStack-method colData,VcfStack-method
> ### colData<-,VcfStack,DataFrame-method rowRanges,RangedVcfStack-method
> ### rowRanges<-,RangedVcfStack,GRanges-method vcfFields,VcfStack-method
> ### assay,VcfStack,ANY-method assay,RangedVcfStack,ANY-method
> ### readVcfStack show,VcfStack-method [,VcfStack,ANY,ANY-method
> ### [,VcfStack,ANY,ANY,ANY-method [,RangedVcfStack,ANY,ANY-method
> ### [,RangedVcfStack,ANY,ANY,ANY-method paths1kg dim,VcfStack-method
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## CONSTRUCTION
> ## ---------------------------------------------------------------------
> ## point to VCF files and add names corresponding to the sequence
> ## present in the file
> extdata <- system.file(package="GenomicFiles", "extdata")
> files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE)
> names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files))
>
> ## input data.frame describing the length of each sequence, coerce to
> ## 'Seqinfo' object
> seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo")
>
> stack <- VcfStack(files, seqinfo)
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
Calls: VcfStack ... VCFHeader -> new -> initialize -> initialize -> validObject
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'GenomicFiles-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VcfStack
> ### Title: VcfStack and RangedVcfStack Objects
> ### Aliases: class:VcfStack VcfStack-class RangedVcfStack-class VcfStack
> ### RangedVcfStack colnames,VcfStack-method rownames,VcfStack-method
> ### dimnames,VcfStack-method files,VcfStack-method
> ### files<-,VcfStack,character-method files<-,VcfStack,VcfFile-method
> ### files<-,VcfStack,VcfFileList-method seqinfo,VcfStack-method
> ### seqinfo<-,VcfStack-method seqinfo<-,RangedVcfStack-method
> ### seqlevelsStyle<-,VcfStack-method
> ### seqlevelsStyle<-,RangedVcfStack-method colData,VcfStack-method
> ### colData<-,VcfStack,DataFrame-method rowRanges,RangedVcfStack-method
> ### rowRanges<-,RangedVcfStack,GRanges-method vcfFields,VcfStack-method
> ### assay,VcfStack,ANY-method assay,RangedVcfStack,ANY-method
> ### readVcfStack show,VcfStack-method [,VcfStack,ANY,ANY-method
> ### [,VcfStack,ANY,ANY,ANY-method [,RangedVcfStack,ANY,ANY-method
> ### [,RangedVcfStack,ANY,ANY,ANY-method paths1kg dim,VcfStack-method
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## CONSTRUCTION
> ## ---------------------------------------------------------------------
> ## point to VCF files and add names corresponding to the sequence
> ## present in the file
> extdata <- system.file(package="GenomicFiles", "extdata")
> files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE)
> names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files))
>
> ## input data.frame describing the length of each sequence, coerce to
> ## 'Seqinfo' object
> seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo")
>
> stack <- VcfStack(files, seqinfo)
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
Calls: VcfStack ... VCFHeader -> new -> initialize -> initialize -> validObject
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'GenomicFiles_unit_tests.R'
ERROR
Running the tests in 'tests/GenomicFiles_unit_tests.R' failed.
Last 13 lines of output:
1 Test Suite :
GenomicFiles RUnit Tests - 12 test functions, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R: Error while sourcing C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R : 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_VcfStack-class.R
C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R
Error in BiocGenerics:::testPackage("GenomicFiles") :
unit tests failed for package GenomicFiles
Execution halted
** running tests for arch 'x64' ...
Running 'GenomicFiles_unit_tests.R'
ERROR
Running the tests in 'tests/GenomicFiles_unit_tests.R' failed.
Last 13 lines of output:
C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R
Error in BiocGenerics:::testPackage("GenomicFiles") :
unit tests failed for package GenomicFiles
Execution halted
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
* 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: 4 ERRORs, 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/GenomicFiles.Rcheck/00check.log'
for details.
GenomicFiles.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/GenomicFiles_1.19.0.tar.gz && rm -rf GenomicFiles.buildbin-libdir && mkdir GenomicFiles.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenomicFiles.buildbin-libdir GenomicFiles_1.19.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GenomicFiles_1.19.0.zip && rm GenomicFiles_1.19.0.tar.gz GenomicFiles_1.19.0.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 290k 100 290k 0 0 1595k 0 --:--:-- --:--:-- --:--:-- 1660k
install for i386
* installing *source* package 'GenomicFiles' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GenomicFiles'
finding HTML links ... done
GenomicFiles-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/GenomicFiles-class.Rd:111: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
GenomicFiles-deprecated html
VcfStack-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:78: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:98: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:129: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:130: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:133: file link 'seqinfo<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:139: file link 'seqlevelsStyle<-' in package 'GenomeInfoDb' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:143: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:148: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:162: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:170: file link 'genotypeToSnpMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:180: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFile' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/VcfStack-class.Rd:227: file link 'VcfFileList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
pack-methods html
reduceByFile-methods html
reduceByRange-methods html
reduceByYield html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/reduceByYield.Rd:12: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/reduceByYield.Rd:29: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/reduceByYield.Rd:121: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpGi6hCc/R.INSTALL190061d1767b/GenomicFiles/man/reduceByYield.Rd:122: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
registry-utils html
unpack-methods html
** 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 'GenomicFiles' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicFiles' as GenomicFiles_1.19.0.zip
* DONE (GenomicFiles)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GenomicFiles' successfully unpacked and MD5 sums checked
|
GenomicFiles.Rcheck/tests_i386/GenomicFiles_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.
> BiocGenerics:::testPackage("GenomicFiles")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
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
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
RUNIT TEST PROTOCOL -- Tue Apr 09 03:10:33 2019
***********************************************
Number of test functions: 12
Number of errors: 1
Number of failures: 0
1 Test Suite :
GenomicFiles RUnit Tests - 12 test functions, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R: Error while sourcing C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R : 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_VcfStack-class.R
C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R
Error in BiocGenerics:::testPackage("GenomicFiles") :
unit tests failed for package GenomicFiles
Execution halted
|
GenomicFiles.Rcheck/tests_x64/GenomicFiles_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.
> BiocGenerics:::testPackage("GenomicFiles")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
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
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
3: In Ops.factor(left, right) : '+' not meaningful for factors
4: In Ops.factor(left, right) : '+' not meaningful for factors
RUNIT TEST PROTOCOL -- Tue Apr 09 03:14:05 2019
***********************************************
Number of test functions: 12
Number of errors: 1
Number of failures: 0
1 Test Suite :
GenomicFiles RUnit Tests - 12 test functions, 1 error, 0 failures
ERROR in C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R: Error while sourcing C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R : 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_VcfStack-class.R
C:/Users/biocbuild/bbs-3.9-bioc/R/library/GenomicFiles/unitTests/test_VcfStack-class.R
Error in BiocGenerics:::testPackage("GenomicFiles") :
unit tests failed for package GenomicFiles
Execution halted
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
Warning messages:
1: In Ops.factor(left, right) : '+' not meaningful for factors
2: In Ops.factor(left, right) : '+' not meaningful for factors
|
|
GenomicFiles.Rcheck/examples_i386/GenomicFiles-Ex.timings
|
GenomicFiles.Rcheck/examples_x64/GenomicFiles-Ex.timings
|