Robert Castelo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/VariantFiltering |
| Branch: RELEASE_3_9 |
| Last Commit: cffc85d |
| Last Changed Date: 2019-05-02 11:53:47 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:04:22 -0400 (Wed, 16 Oct 2019).
| Package 1707/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| VariantFiltering 1.20.0 Robert Castelo
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: VariantFiltering |
| Version: 1.20.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:VariantFiltering.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings VariantFiltering_1.20.0.tar.gz |
| StartedAt: 2019-10-16 05:40:17 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:47:37 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 440.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: VariantFiltering.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:VariantFiltering.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings VariantFiltering_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/VariantFiltering.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VariantFiltering/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantFiltering’ version ‘1.20.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘VariantFiltering’ can be installed ... OK * 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 * 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 ... NOTE annotateVariants,MafDb: no visible global function definition for 'mafByOverlaps' Undefined global functions or variables: mafByOverlaps * 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/VariantFiltering.Rcheck/00check.log’ for details.
VariantFiltering.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL VariantFiltering ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘VariantFiltering’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c methods-WeightMatrix.c -o methods-WeightMatrix.o gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-VariantFiltering/00new/VariantFiltering/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for 'annotateVariants' with signature 'annObj="MafDb"': no definition for class "MafDb" ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (VariantFiltering)
VariantFiltering.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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
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 -- Wed Oct 16 05:47:33 2019
***********************************************
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 `seqlevelsStyle<-`(`*tmp*`, value = value) :
more than one seqlevels style supplied, using the 1st one only
2: 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.
3: In `seqlevelsStyle<-`(`*tmp*`, value = value) :
more than one seqlevels style supplied, using the 1st one only
4: In `seqlevelsStyle<-`(`*tmp*`, value = value) :
more than one seqlevels style supplied, using the 1st one only
5: In annotationEngine(variants, param, annotationCache, BPPARAM = BPPARAM) :
Assumming hg19 and hs37d5 represent the same genome build.
6: 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.
7: In `seqlevelsStyle<-`(`*tmp*`, value = value) :
more than one seqlevels style supplied, using the 1st one only
8: In .scoreBindingSiteVariants(variantsVR_annotated, weightMatrices, :
Assumming hg19 and hs37d5 represent the same genome build.
9: In recycleSingleBracketReplacementValue(value, x, nsbs) :
number of values supplied is not a sub-multiple of the number of values to be replaced
10: 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
96.262 2.241 99.727
VariantFiltering.Rcheck/VariantFiltering-Ex.timings
| name | user | system | elapsed | |
| GenePhylostrataDb-class | 0 | 0 | 0 | |
| VariantFilteringParam-class | 4.168 | 0.352 | 4.564 | |
| VariantFilteringResults-class | 0 | 0 | 0 | |
| VariantType-class | 0.000 | 0.001 | 0.000 | |
| WeightMatrix-class | 0.010 | 0.002 | 0.024 | |
| autosomalDominant | 0.001 | 0.000 | 0.000 | |
| autosomalRecessiveHeterozygous | 0 | 0 | 0 | |
| autosomalRecessiveHomozygous | 0 | 0 | 0 | |
| deNovo | 0 | 0 | 0 | |
| readAAradicalChangeMatrix | 0.003 | 0.000 | 0.003 | |
| unrelatedIndividuals | 0 | 0 | 0 | |
| xLinked | 0 | 0 | 0 | |