##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicAlignments.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicAlignments_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicAlignments.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomicAlignments/DESCRIPTION' ... OK
* this is package 'GenomicAlignments' version '1.35.0'
* 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
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* 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 ... WARNING
checkRd: (5) GAlignmentPairs-class.Rd:90-94: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:102-133: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:134-137: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:138-143: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:144-160: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:161-172: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:173-179: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:180-183: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:184-188: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:189-193: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:194-203: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:204-210: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:211-216: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:217-222: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:223-232: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:240-244: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:252-257: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:258-264: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:272-298: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:299-328: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:329-336: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:337-340: \item in \describe must have non-empty label
checkRd: (5) GAlignmentPairs-class.Rd:348-359: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:148-154: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:162-165: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:166-171: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:172-179: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:180-183: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:184-190: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:191-195: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:196-202: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:203-213: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:214-221: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:222-227: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:228-232: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:233-241: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:242-248: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:249-254: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:255-260: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:261-270: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:278-292: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:293-335: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:336-344: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:351-357: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:365-369: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:375-381: \item in \describe must have non-empty label
checkRd: (5) GAlignments-class.Rd:388-400: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:67-70: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:78-81: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:82-85: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:86-90: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:91-94: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:95-99: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:100-105: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:106-112: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:113-118: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:119-123: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:124-129: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:130-134: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:135-139: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:140-146: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:147-152: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:153-158: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:170-187: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:188-206: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:207-215: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:216-222: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:223-228: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:236-240: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:241-244: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:245-250: \item in \describe must have non-empty label
checkRd: (5) GAlignmentsList-class.Rd:256-262: \item in \describe must have non-empty label
checkRd: (5) GappedReads-class.Rd:40-44: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:133-137: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:138-155: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:156-182: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:183-185: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:186-192: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:200-204: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:213-227: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:228-235: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:236-245: \item in \describe must have non-empty label
checkRd: (5) OverlapEncodings-class.Rd:246-261: \item in \describe must have non-empty label
checkRd: (5) summarizeOverlaps-methods.Rd:226-246: \item in \describe must have non-empty label
* 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-3.17-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 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
junctions-methods          11.69   1.37   13.61
readGAlignments             9.66   0.35   17.00
sequenceLayer               7.40   0.95    8.45
summarizeOverlaps-methods   6.74   0.19   57.69
coordinate-mapping-methods  6.12   0.20    6.38
* 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: 1 WARNING, 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicAlignments.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenomicAlignments
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'GenomicAlignments' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:676:30: warning: 'f_elt' may be used uninitialized [-Wmaybe-uninitialized]
  676 |                         f_elt++;
      |                         ~~~~~^~
cigar_utils.c:593:41: note: 'f_elt' was declared here
  593 |         const int *flag_elt, *pos_elt, *f_elt;
      |                                         ^~~~~
In function 'parse_cigar_ranges',
    inlined from 'cigar_ranges' at cigar_utils.c:660:12:
cigar_utils.c:213:21: warning: 'range_buf1' may be used uninitialized [-Wmaybe-uninitialized]
  213 |         buf_nelt0 = IntPairAE_get_nelt(range_buf);
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:590:20: note: 'range_buf1' was declared here
  590 |         IntPairAE *range_buf1;
      |                    ^~~~~~~~~~
cigar_utils.c:674:37: warning: 'breakpoint' may be used uninitialized [-Wmaybe-uninitialized]
  674 |                         *(breakpoint++) = IntPairAE_get_nelt(range_buf1);
      |                          ~~~~~~~~~~~^~~
cigar_utils.c:588:62: note: 'breakpoint' was declared here
  588 |         int cigar_len, space0, pos_len, f_is_NULL, ans_len, *breakpoint,
      |                                                              ^~~~~~~~~~
cigar_utils.c:542:25: warning: 'ans_breakpoints' may be used uninitialized [-Wmaybe-uninitialized]
  542 |                         new_PartitioningByEnd("PartitioningByEnd",
      |                         ^~~~~~~~~~~~~~~~~~~~~
cigar_utils.c:587:19: note: 'ans_breakpoints' was declared here
  587 |         SEXP ans, ans_breakpoints, f_levels, cigar_elt;
      |                   ^~~~~~~~~~~~~~~
cigar_utils.c:626:29: warning: 'flag_elt' may be used uninitialized [-Wmaybe-uninitialized]
  626 |                         if (*flag_elt == NA_INTEGER) {
      |                             ^~~~~~~~~
cigar_utils.c:593:20: note: 'flag_elt' was declared here
  593 |         const int *flag_elt, *pos_elt, *f_elt;
      |                    ^~~~~~~~
cigar_utils.c: In function 'cigar_width':
cigar_utils.c:708:29: warning: 'flag_elt' may be used uninitialized [-Wmaybe-uninitialized]
  708 |                         if (*flag_elt == NA_INTEGER) {
      |                             ^~~~~~~~~
cigar_utils.c:698:20: note: 'flag_elt' was declared here
  698 |         const int *flag_elt;
      |                    ^~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
coordinate_mapping_methods.c: In function 'to_query':
coordinate_mapping_methods.c:64:26: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
   64 |   if (query_loc < 0 || n == 0)
      |                        ~~^~~~
coordinate_mapping_methods.c:17:7: note: 'n' was declared here
   17 |   int n, offset = 0, OPL, query_consumed = 0;
      |       ^
coordinate_mapping_methods.c: In function 'to_ref':
coordinate_mapping_methods.c:219:6: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
  219 |   if (n == 0)
      |      ^
coordinate_mapping_methods.c:172:7: note: 'n' was declared here
  172 |   int n, offset = 0, OPL, query_consumed = 0;
      |       ^
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/IRanges/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/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 (GenomicAlignments)

R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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, 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, 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 Dec 29 00:08:48 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 
  20.51    0.59   36.67