##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicAlignments.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicAlignments_1.31.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GenomicAlignments.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenomicAlignments/DESCRIPTION' ... OK
* this is package 'GenomicAlignments' version '1.31.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'Rsamtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GenomicAlignments' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'BiocGenerics' 'S4Vectors' 'IRanges' 'GenomicRanges' 'Biostrings' 'Rsamtools'
A package should be listed in only one of these fields.
* 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
':::' calls which should be '::':
  'S4Vectors:::makeClassinfoRowForCompactPrinting'
  'S4Vectors:::makePrettyMatrixForCompactPrinting'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'Biostrings:::.normarg_padding.letter'
  'Rsamtools:::.BamViews_delegate' 'Rsamtools:::.findMateWithinGroups'
  'Rsamtools:::.load_bamcols_from_scanBam_res'
  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 ... 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/GenomicAlignments/libs/x64/GenomicAlignments.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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
junctions-methods          11.55   1.86   13.59
readGAlignments             9.68   0.94   17.79
summarizeOverlaps-methods   6.78   0.20   55.62
coordinate-mapping-methods  6.41   0.28    6.69
sequenceLayer               5.14   0.96    6.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'run_unitTests.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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/GenomicAlignments.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GenomicAlignments' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c IRanges_stubs.c -o IRanges_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:9: warning: 'f_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    f_elt++;
    ~~~~~^~
cigar_utils.c:674:22: warning: 'range_buf1' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:674:16: warning: 'breakpoint' may be used uninitialized in this function [-Wmaybe-uninitialized]
    *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
     ~~~~~~~~~~~^~~
cigar_utils.c:626:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (*flag_elt == NA_INTEGER) {
        ^~~~~~~~~
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:8: warning: 'flag_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (*flag_elt == NA_INTEGER) {
        ^~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/S4Vectors/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/IRanges/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
encodeOverlaps_methods.c: In function 'overlap_encoding':
encodeOverlaps_methods.c:180:33: warning: 'out_nelt0' may be used uninitialized in this function [-Wmaybe-uninitialized]
  CharAE_set_nelt(out, out_nelt0 + j2 * nrow);
                       ~~~~~~~~~~^~~~~~~~~~~
encodeOverlaps_methods.c:99:6: note: 'out_nelt0' was declared here
  int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      ^~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o GenomicAlignments.dll tmp.def IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenomicAlignments'
    finding HTML links ... done
    GAlignmentPairs-class                   html  
    finding level-2 HTML links ... done

    GAlignments-class                       html  
    GAlignmentsList-class                   html  
    GappedReads-class                       html  
    OverlapEncodings-class                  html  
    cigar-utils                             html  
    coordinate-mapping-methods              html  
    coverage-methods                        html  
    encodeOverlaps-methods                  html  
    findCompatibleOverlaps-methods          html  
    findMateAlignment                       html  
    findOverlaps-methods                    html  
    findSpliceOverlaps-methods              html  
    intra-range-methods                     html  
    junctions-methods                       html  
    pileLettersAt                           html  
    readGAlignments                         html  
    sequenceLayer                           html  
    setops-methods                          html  
    stackStringsFromGAlignments             html  
    summarizeOverlaps-methods               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicAlignments)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'seq2pathway' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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.

> require("GenomicAlignments") || stop("unable to load GenomicRanges package")
Loading required package: GenomicAlignments
Loading required package: BiocGenerics

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, 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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
[1] TRUE
> GenomicAlignments:::.test()


RUNIT TEST PROTOCOL -- Thu Mar 17 19:15:21 2022 
*********************************************** 
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomicAlignments RUnit Tests - 42 test functions, 0 errors, 0 failures
Number of test functions: 42 
Number of errors: 0 
Number of failures: 0 
Warning message:
In .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode,  :
    4 alignments with ambiguous pairing were dumped.
    Use 'getDumpedAlignments()' to retrieve them from the dump environment.
> 
> proc.time()
   user  system elapsed 
  21.04    0.92   36.86