Robert Castelo
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/VariantFiltering |
| Branch: RELEASE_3_12 |
| Last Commit: 3acde0e |
| Last Changed Date: 2020-10-27 10:56:11 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:09 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the VariantFiltering package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1932/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantFiltering 1.26.0 (landing page) Robert Castelo
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: VariantFiltering |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantFiltering.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings VariantFiltering_1.26.0.tar.gz |
| StartedAt: 2021-05-06 07:51:05 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 08:04:20 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 795.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: VariantFiltering.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VariantFiltering.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings VariantFiltering_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantFiltering.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VariantFiltering/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VariantFiltering' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'VariantFiltering' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/GenePhylostrataDb-class.Rd:47: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringParam-class.Rd:105: file link 'getGeneticCode' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringParam-class.Rd:123: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:81: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:84: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:101: file link 'isSNV' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:102: file link 'isInsertion' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:103: file link 'isDeletion' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:104: file link 'isSubstitution' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:105: file link 'isDelins' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:120: file link 'predictCoding' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:198: file link 'graphNEL' in package 'graph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:201: file link 'nodeData' in package 'graph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:207: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:211: file link 'VRangesList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:215: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:228: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:235: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:254: file link 'softFilterMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:316: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:317: file link 'predictCoding' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:332: file link 'AlignmentsTrack' in package 'Gviz' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantType-class.Rd:40: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantType-class.Rd:56: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantType-class.Rd:60: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalDominant.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalDominant.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalDominant.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:22: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:26: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:28: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalRecessiveHomozygous.Rd:26: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/deNovo.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/deNovo.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/deNovo.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/unrelatedIndividuals.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/unrelatedIndividuals.Rd:27: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/unrelatedIndividuals.Rd:29: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/xLinked.Rd:24: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/xLinked.Rd:30: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/xLinked.Rd:32: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantFiltering.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
R 1.0Mb
extdata 3.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'S4Vectors:::labeledLine' 'VariantAnnotation:::.checkArgs'
'VariantAnnotation:::.consolidateHits'
'VariantAnnotation:::.returnEmpty'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.adjustForStrandSense' '.ancestorsSO' '.findSOIDs'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/VariantFiltering/libs/i386/VariantFiltering.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/VariantFiltering/libs/x64/VariantFiltering.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
VariantFilteringParam-class 9.64 5.25 15.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
VariantFilteringParam-class 9.44 3.33 13
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantFiltering.Rcheck/00check.log'
for details.
VariantFiltering.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/VariantFiltering_1.26.0.tar.gz && rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VariantFiltering.buildbin-libdir VariantFiltering_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.26.0.zip && rm VariantFiltering_1.26.0.tar.gz VariantFiltering_1.26.0.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 3207k 100 3207k 0 0 29.9M 0 --:--:-- --:--:-- --:--:-- 30.4M
install for i386
* installing *source* package 'VariantFiltering' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c methods-WeightMatrix.c -o methods-WeightMatrix.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantFiltering.buildbin-libdir/00LOCK-VariantFiltering/00new/VariantFiltering/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'VariantFiltering'
finding HTML links ... done
GenePhylostrataDb-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/GenePhylostrataDb-class.Rd:47: file link 'phastCons100way.UCSC.hg19' in package 'phastCons100way.UCSC.hg19' does not exist and so has been treated as a topic
VariantFiltering-defunct html
VariantFiltering-deprecated html
finding level-2 HTML links ... done
VariantFiltering-package html
VariantFilteringParam-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringParam-class.Rd:105: file link 'getGeneticCode' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringParam-class.Rd:123: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
VariantFilteringResults-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:81: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:84: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:101: file link 'isSNV' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:102: file link 'isInsertion' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:103: file link 'isDeletion' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:104: file link 'isSubstitution' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:105: file link 'isDelins' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:120: file link 'predictCoding' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:198: file link 'graphNEL' in package 'graph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:201: file link 'nodeData' in package 'graph' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:207: file link 'BamViews' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:211: file link 'VRangesList' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:215: file link 'VRanges' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:228: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:235: file link 'FilterRules' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:254: file link 'softFilterMatrix' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:316: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:317: file link 'predictCoding' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantFilteringResults-class.Rd:332: file link 'AlignmentsTrack' in package 'Gviz' does not exist and so has been treated as a topic
VariantType-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantType-class.Rd:40: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantType-class.Rd:56: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/VariantType-class.Rd:60: file link 'locateVariants' in package 'VariantAnnotation' does not exist and so has been treated as a topic
WeightMatrix-class html
autosomalDominant html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalDominant.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalDominant.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalDominant.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
autosomalRecessiveHeterozygous html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:22: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:26: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalRecessiveHeterozygous.Rd:28: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
autosomalRecessiveHomozygous html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/autosomalRecessiveHomozygous.Rd:26: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
deNovo html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/deNovo.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/deNovo.Rd:29: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/deNovo.Rd:31: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
readAAradicalChangeMatrix html
unrelatedIndividuals html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/unrelatedIndividuals.Rd:23: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/unrelatedIndividuals.Rd:27: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/unrelatedIndividuals.Rd:29: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
xLinked html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/xLinked.Rd:24: file link 'readVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/xLinked.Rd:30: file link 'BiocParallelParam' in package 'BiocParallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpG4iX6j/R.INSTALL2888598b5fba/VariantFiltering/man/xLinked.Rd:32: file link 'bpparam' in package 'BiocParallel' 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 'VariantFiltering' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c methods-WeightMatrix.c -o methods-WeightMatrix.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/VariantFiltering.buildbin-libdir/VariantFiltering/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantFiltering' as VariantFiltering_1.26.0.zip
* DONE (VariantFiltering)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'VariantFiltering' successfully unpacked and MD5 sums checked
|
VariantFiltering.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("VariantFiltering")
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.max, which.min
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Loading BSgenome annotation package BSgenome.Hsapiens.1000genomes.hs37d5
Loading OrgDb annotation package org.Hs.eg.db
Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene
Assuming the genome build of the input variants is hs37d5.
Switching to the UCSC chromosome-name style from the transcript-centric annotation package.
Chromosome chrM has different lengths between the input VCF and the input TxDb pakage. This chromosome will be discarded from further analysis
Assumming hs37d5 and hg19 represent the same genome build.
Discarding scaffold sequences.
Annotating variant type (SNV, Insertion, Deletion, MNV, Delins)
Annotating location with VariantAnnotation::locateVariants()
Annotating coding variants VariantAnnotation::predictCoding()
Annotating codon usage frequencies in coding synonymous variants
Scoring binding sites with weight matrix donorSites.
Scoring binding sites with weight matrix acceptorSites.
1000 variants processed
RUNIT TEST PROTOCOL -- Thu May 06 08:02:31 2021
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
VariantFiltering RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 597 out-of-bound ranges located on sequences
29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222,
72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544,
73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674,
76675, 76676, 76677, 76679, and 76680. Note that ranges located on a
sequence whose length is unknown (NA) or on a circular sequence are not
considered out-of-bound (use seqlengths() and isCircular() to get the
lengths and circularity flags of the underlying sequences). You can use
trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more
information.
2: In annotationEngine(variants, param, annotationCache, BPPARAM = BPPARAM) :
Assumming GRCh37.p13 and hs37d5 represent the same genome build.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 597 out-of-bound ranges located on sequences
29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222,
72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544,
73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674,
76675, 76676, 76677, 76679, and 76680. Note that ranges located on a
sequence whose length is unknown (NA) or on a circular sequence are not
considered out-of-bound (use seqlengths() and isCircular() to get the
lengths and circularity flags of the underlying sequences). You can use
trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more
information.
4: In .scoreBindingSiteVariants(variantsVR_annotated, weightMatrices, :
Assumming GRCh37.p13 and hs37d5 represent the same genome build.
5: In recycleSingleBracketReplacementValue(value, x, nsbs) :
number of values supplied is not a sub-multiple of the number of values to be replaced
6: In recycleSingleBracketReplacementValue(value, x, nsbs) :
number of values supplied is not a sub-multiple of the number of values to be replaced
>
> proc.time()
user system elapsed
98.35 10.65 116.85
|
VariantFiltering.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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("VariantFiltering")
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.max, which.min
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
Loading BSgenome annotation package BSgenome.Hsapiens.1000genomes.hs37d5
Loading OrgDb annotation package org.Hs.eg.db
Loading TxDb annotation package TxDb.Hsapiens.UCSC.hg19.knownGene
Assuming the genome build of the input variants is hs37d5.
Switching to the UCSC chromosome-name style from the transcript-centric annotation package.
Chromosome chrM has different lengths between the input VCF and the input TxDb pakage. This chromosome will be discarded from further analysis
Assumming hs37d5 and hg19 represent the same genome build.
Discarding scaffold sequences.
Annotating variant type (SNV, Insertion, Deletion, MNV, Delins)
Annotating location with VariantAnnotation::locateVariants()
Annotating coding variants VariantAnnotation::predictCoding()
Annotating codon usage frequencies in coding synonymous variants
Scoring binding sites with weight matrix donorSites.
Scoring binding sites with weight matrix acceptorSites.
1000 variants processed
RUNIT TEST PROTOCOL -- Thu May 06 08:04:14 2021
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
VariantFiltering RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 597 out-of-bound ranges located on sequences
29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222,
72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544,
73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674,
76675, 76676, 76677, 76679, and 76680. Note that ranges located on a
sequence whose length is unknown (NA) or on a circular sequence are not
considered out-of-bound (use seqlengths() and isCircular() to get the
lengths and circularity flags of the underlying sequences). You can use
trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more
information.
2: In annotationEngine(variants, param, annotationCache, BPPARAM = BPPARAM) :
Assumming GRCh37.p13 and hs37d5 represent the same genome build.
3: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 597 out-of-bound ranges located on sequences
29194, 29195, 29196, 72038, 72039, 72040, 72041, 72044, 72220, 72222,
72223, 72224, 71343, 71344, 73323, 73324, 73326, 72882, 72883, 74544,
73782, 73852, 74055, 74056, 74057, 74058, 74171, 75259, 76673, 76674,
76675, 76676, 76677, 76679, and 76680. Note that ranges located on a
sequence whose length is unknown (NA) or on a circular sequence are not
considered out-of-bound (use seqlengths() and isCircular() to get the
lengths and circularity flags of the underlying sequences). You can use
trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more
information.
4: In .scoreBindingSiteVariants(variantsVR_annotated, weightMatrices, :
Assumming GRCh37.p13 and hs37d5 represent the same genome build.
5: In recycleSingleBracketReplacementValue(value, x, nsbs) :
number of values supplied is not a sub-multiple of the number of values to be replaced
6: In recycleSingleBracketReplacementValue(value, x, nsbs) :
number of values supplied is not a sub-multiple of the number of values to be replaced
>
> proc.time()
user system elapsed
90.96 6.85 101.65
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VariantFiltering.Rcheck/examples_i386/VariantFiltering-Ex.timings
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VariantFiltering.Rcheck/examples_x64/VariantFiltering-Ex.timings
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