##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VariantFiltering.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings VariantFiltering_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/VariantFiltering.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'VariantFiltering/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VariantFiltering' version '1.39.0'
* 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 ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) VariantFiltering-deprecated.Rd:87: Lost braces
    87 |     \item{dbSNPpresent(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                              ^
checkRd: (-1) VariantFiltering-deprecated.Rd:88: Lost braces
    88 |     \item{OMIMpresent(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                             ^
checkRd: (-1) VariantFiltering-deprecated.Rd:89: Lost braces
    89 |     \item{variantType(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                             ^
checkRd: (-1) VariantFiltering-deprecated.Rd:90: Lost braces
    90 |     \item{aaChangeType(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                              ^
checkRd: (-1) VariantFiltering-deprecated.Rd:91: Lost braces
    91 |     \item{variantLocation(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                                 ^
checkRd: (-1) VariantFiltering-deprecated.Rd:92: Lost braces
    92 |     \item{variantConsequence(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                                    ^
checkRd: (-1) VariantFiltering-deprecated.Rd:93: Lost braces
    93 |     \item{naMAF(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                       ^
checkRd: (-1) VariantFiltering-deprecated.Rd:94: Lost braces
    94 |     \item{MAFpop(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                        ^
checkRd: (-1) VariantFiltering-deprecated.Rd:95: Lost braces
    95 |     \item{maxMAF(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                        ^
checkRd: (-1) VariantFiltering-deprecated.Rd:96: Lost braces
    96 |     \item{minPhastCons(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                              ^
checkRd: (-1) VariantFiltering-deprecated.Rd:97: Lost braces
    97 |     \item{minPhylostratum(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                                 ^
checkRd: (-1) VariantFiltering-deprecated.Rd:98: Lost braces
    98 |     \item{minScore5ss(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                             ^
checkRd: (-1) VariantFiltering-deprecated.Rd:99: Lost braces
    99 |     \item{minScore3ss(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                             ^
checkRd: (-1) VariantFiltering-deprecated.Rd:100: Lost braces
   100 |     \item{minCUfc(): This functionality is now replaced by the combined used of functions \code{\link{filters}()}, \code{\link{active}()}, \code{\link{cutoffs}()}, code{\link{change}()}}
       |                                                                                                                                                                         ^
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/VariantFiltering/libs/x64/VariantFiltering.dll':
  Found '_exit', possibly from '_exit' (C)
  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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
VariantFilteringParam-class 10.36   6.23   17.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/VariantFiltering.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL VariantFiltering
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'VariantFiltering' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-VariantFiltering/00new/VariantFiltering/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (VariantFiltering)

R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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:stats':

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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, 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:utils':

    findMatches

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

    I, expand.grid, unname


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 Mar 28 07:55:18 2024 
*********************************************** 
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 (function (seqlevels, genome, new_style)  :
  cannot switch some hg19's seqlevels from UCSC to NCBI style
3: In annotationEngine(variants, param, annotationCache, BPPARAM = BPPARAM) :
  Assumming GRCh37.p13 and hs37d5 represent the same genome build.
4: 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.
5: In .scoreBindingSiteVariants(variantsVR_annotated, weightMatrices,  :
  Assumming GRCh37.p13 and hs37d5 represent the same genome build.
6: In recycleSingleBracketReplacementValue(value, x, nsbs) :
  number of values supplied is not a sub-multiple of the number of values to be replaced
7: 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 
  88.84   12.70  108.51