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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GenomicAlignments_1.41.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GenomicAlignments.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* this is package ‘GenomicAlignments’ version ‘1.41.0’
* 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: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 ... 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
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 ... NOTE
checkRd: (-1) coordinate-mapping-methods.Rd:69-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coordinate-mapping-methods.Rd:84-101: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coordinate-mapping-methods.Rd:102-114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coordinate-mapping-methods.Rd:115-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findSpliceOverlaps-methods.Rd:99-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findSpliceOverlaps-methods.Rd:103-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findSpliceOverlaps-methods.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) intra-range-methods.Rd:52-60: Lost braces
    52 |     \item(){
       |            ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
readGAlignments            10.916  0.626  11.501
junctions-methods           8.892  0.240   9.198
summarizeOverlaps-methods   4.292  1.961   5.848
coordinate-mapping-methods  5.605  0.088   5.712
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/GenomicAlignments.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GenomicAlignments
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c cigar_utils.c -o cigar_utils.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/include/Rdefines.h:41,
                 from GenomicAlignments.h:1,
                 from cigar_utils.c:1:
In function ‘make_CompressedIRangesList’,
    inlined from ‘cigar_ranges’ at cigar_utils.c:680:2:
cigar_utils.c:534:25: warning: ‘range_buf1’ may be used uninitialized [-Wmaybe-uninitialized]
  534 |                         new_IRanges_from_IntPairAE("IRanges", range_buf));
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
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: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:656:29: warning: ‘f_elt’ may be used uninitialized [-Wmaybe-uninitialized]
  656 |                         if (*f_elt == NA_INTEGER)
      |                             ^~~~~~
cigar_utils.c:593:41: note: ‘f_elt’ was declared here
  593 |         const int *flag_elt, *pos_elt, *f_elt;
      |                                         ^~~~~
In function ‘make_CompressedIRangesList’,
    inlined from ‘cigar_ranges’ at cigar_utils.c:680:2:
cigar_utils.c:542:25: warning: ‘ans_breakpoints’ may be used uninitialized [-Wmaybe-uninitialized]
  542 |                         new_PartitioningByEnd("PartitioningByEnd",
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  543 |                                               breakpoints, NULL));
      |                                               ~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/include/Rinternals.h:371:36: note: in definition of macro ‘PROTECT’
  371 | #define PROTECT(s)      Rf_protect(s)
      |                                    ^
cigar_utils.c: In function ‘cigar_ranges’:
cigar_utils.c:587:19: note: ‘ans_breakpoints’ was declared here
  587 |         SEXP ans, ans_breakpoints, f_levels, cigar_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;
      |                    ^~~~~~~~
In function ‘narrow_cigar_string’,
    inlined from ‘cigar_narrow’ at cigar_utils.c:920:12:
cigar_utils.c:872:12: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized]
  872 |         if (Roffset < Loffset) {
      |            ^
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:854:13: note: ‘Loffset’ was declared here
  854 |         int Loffset, Roffset, buf_offset;
      |             ^~~~~~~
In function ‘narrow_cigar_string’,
    inlined from ‘cigar_narrow’ at cigar_utils.c:920:12:
cigar_utils.c:872:12: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized]
  872 |         if (Roffset < Loffset) {
      |            ^
cigar_utils.c: In function ‘cigar_narrow’:
cigar_utils.c:854:22: note: ‘Roffset’ was declared here
  854 |         int Loffset, Roffset, buf_offset;
      |                      ^~~~~~~
In function ‘qnarrow_cigar_string’,
    inlined from ‘cigar_qnarrow’ at cigar_utils.c:1116:12:
cigar_utils.c:1063:12: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized]
 1063 |         if (Roffset < Loffset) {
      |            ^
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1045:13: note: ‘Loffset’ was declared here
 1045 |         int Loffset, Roffset, buf_offset;
      |             ^~~~~~~
In function ‘qnarrow_cigar_string’,
    inlined from ‘cigar_qnarrow’ at cigar_utils.c:1116:12:
cigar_utils.c:1063:12: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized]
 1063 |         if (Roffset < Loffset) {
      |            ^
cigar_utils.c: In function ‘cigar_qnarrow’:
cigar_utils.c:1045:22: note: ‘Roffset’ was declared here
 1045 |         int Loffset, Roffset, buf_offset;
      |                      ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
In function ‘unsafe_overlap_encoding’,
    inlined from ‘overlap_encoding’ at encodeOverlaps_methods.c:209:2:
encodeOverlaps_methods.c:182:9: warning: ‘out_nelt0’ may be used uninitialized [-Wmaybe-uninitialized]
  182 |         CharAE_delete_at(out, out_nelt0, j1 * nrow);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
encodeOverlaps_methods.c: In function ‘overlap_encoding’:
encodeOverlaps_methods.c:99:13: note: ‘out_nelt0’ was declared here
   99 |         int out_nelt0, i, starti, widthi, spacei, j, startj, widthj, spacej,
      |             ^~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, 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 -- Thu Sep 12 00:54:00 2024 
*********************************************** 
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 
 18.914   1.256  19.854