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CHECK report for VariantAnnotation on malbec1

This page was generated on 2018-04-12 13:09:45 -0400 (Thu, 12 Apr 2018).

Package 1443/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.24.5
Valerie Obenchain
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/VariantAnnotation
Branch: RELEASE_3_6
Last Commit: 468d7f5
Last Changed Date: 2018-01-04 14:55:50 -0400 (Thu, 04 Jan 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.24.5
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.24.5.tar.gz
StartedAt: 2018-04-12 03:31:43 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:38:40 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 417.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: VariantAnnotation.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings VariantAnnotation_1.24.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantAnnotation’ version ‘1.24.5’
* 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 ‘VariantAnnotation’ 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
'library' or 'require' call to ‘snpStats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’ ‘BiocGenerics:::testPackage’
  ‘Rsamtools:::.RsamtoolsFile’ ‘Rsamtools:::.RsamtoolsFileList’
  ‘Rsamtools:::.io_check_exists’ ‘S4Vectors:::expandByColumnSet’
  ‘S4Vectors:::labeledLine’ ‘S4Vectors:::recycleVector’
  ‘S4Vectors:::selectSome’
  ‘SummarizedExperiment:::.SummarizedExperiment.charbound’
  ‘SummarizedExperiment:::.cbind.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 ... NOTE
.predictCodingGRangesList: no visible binding for global variable
  ‘GENETIC_CODE’
VRangesForMatching: no visible binding for global variable ‘REF’
VRangesForMatching: no visible binding for global variable ‘ALT’
probabilityToSnpMatrix: no visible global function definition for
  ‘post2g’
import,VcfFile-ANY-ANY: no visible global function definition for
  ‘checkArgFormat’
Undefined global functions or variables:
  ALT GENETIC_CODE REF checkArgFormat post2g
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'mcols<-' and siglist 'VCF'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘VariantAnnotation/libs/VariantAnnotation.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
predictCoding-methods     20.380  0.016  20.412
locateVariants-methods    19.684  0.200  19.893
PROVEANDb-class            6.056  0.608   9.193
summarizeVariants-methods  5.876  0.000   5.880
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘VariantAnnotation_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.



Installation output

VariantAnnotation.Rcheck/00install.out

* installing *source* package ‘VariantAnnotation’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c dna_hash.c -o dna_hash.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rle.c -o rle.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c strhash.c -o strhash.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c vcffile.c -o vcffile.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c vcftype.c -o vcftype.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c writevcf.c -o writevcf.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/VariantAnnotation.Rcheck/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantAnnotation)

Tests output

VariantAnnotation.Rcheck/tests/VariantAnnotation_unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

> require("VariantAnnotation") || stop("unable to load VariantAnnotation package")
Loading required package: VariantAnnotation
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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: GenomeInfoDb
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
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

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

[1] TRUE
> VariantAnnotation:::.test()
Loading required package: RSQLite
Loading required package: survival
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:VariantAnnotation':

    expand

The following object is masked from 'package:S4Vectors':

    expand

non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
'select()' returned 1:1 mapping between keys and columns
Loading required package: BSgenome
Loading required package: rtracklayer
'select()' returned many:1 mapping between keys and columns


RUNIT TEST PROTOCOL -- Thu Apr 12 03:38:36 2018 
*********************************************** 
Number of test functions: 92 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
VariantAnnotation RUnit Tests - 92 test functions, 0 errors, 0 failures
Number of test functions: 92 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: info fields with no header: noMatch 
2: In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
3: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion
> 
> proc.time()
   user  system elapsed 
127.168   0.764 129.116 

Example timings

VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings

nameusersystemelapsed
GLtoGP2.1720.1402.315
PROVEANDb-class6.0560.6089.193
PolyPhenDb-class0.7680.0442.881
SIFTDb-class0.0000.0000.001
ScanVcfParam-class1.0000.0361.037
VCF-class1.4560.0041.461
VCFHeader-class0.0560.0000.057
VRanges-class0.6320.0000.634
VRangesList-class0.6720.0000.674
VariantType-class0.0080.0000.011
VcfFile-class0.4760.0000.475
filterVcf-methods3.1440.0523.202
genotypeToSnpMatrix-methods0.8240.0880.911
getTranscriptSeqs-methods0.0000.0000.001
indexVcf-method0.0080.0000.008
isSNV-methods0.8280.0000.828
locateVariants-methods19.684 0.20019.893
predictCoding-methods20.380 0.01620.412
probabilityToSnpMatrix0.040.000.04
readVcf-methods1.7320.0081.745
scanVcf-methods0.1480.0000.149
seqinfo-method0.0360.0000.036
snpSummary0.1840.0000.184
summarizeVariants-methods5.8760.0005.880
writeVcf-methods0.9240.0040.928