##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicAlignments_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenomicAlignments.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* this is package ‘GenomicAlignments’ version ‘1.36.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicAlignments’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since
  Cannot process chunk/lines:
    version 1.18.0
  Cannot process chunk/lines:
    No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since
  Cannot process chunk/lines:
    version 1.16.0
  Cannot process chunk/lines:
    The first version of GenomicAlignments was included in Bioconductor 2.14. 
  Cannot process chunk/lines:
    The package was created from existing code in IRanges, ShortRead, 
  Cannot process chunk/lines:
    Rsamtools and GenomicRanges. 
* 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:
  ‘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 is not available
* 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
readGAlignments             15.059  2.067  25.793
junctions-methods           14.429  1.193  22.024
summarizeOverlaps-methods    8.512  1.587  15.076
coordinate-mapping-methods   8.626  0.287  13.373
sequenceLayer                6.279  0.801  10.811
findSpliceOverlaps-methods   5.733  0.166   8.606
stackStringsFromGAlignments  4.567  0.200   7.302
* 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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenomicAlignments.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicAlignments
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cigar_utils.c -o cigar_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/IRanges/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** 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
** 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 (GenomicAlignments)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
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 -- Tue Oct 17 21:39:44 2023 
*********************************************** 
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 
 29.977   1.264  47.475