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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings GenomicAlignments_1.43.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GenomicAlignments.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK
* this is package ‘GenomicAlignments’ version ‘1.43.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GAlignmentPairs-class.Rd: seqlevels, GRanges, GRangesList
  GAlignments-class.Rd: seqlevels, GRanges, GRangesList
  GAlignmentsList-class.Rd: GRanges, GRangesList
  coordinate-mapping-methods.Rd: GenomicRanges-class
  findCompatibleOverlaps-methods.Rd: GRangesList
  findOverlaps-methods.Rd: GRangesList, GRanges-class,
    GRangesList-class
  intra-range-methods.Rd: GRanges, GRangesList
  readGAlignments.Rd: scanBam, ScanBamParam-class
  sequenceLayer.Rd: XStringSet
  stackStringsFromGAlignments.Rd: scanBam, ScanBamParam
  summarizeOverlaps-methods.Rd: BamFile, ScanBamParam, register
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... ERROR
Running examples in ‘GenomicAlignments-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: junctions-methods
> ### Title: Extract junctions from genomic alignments
> ### Aliases: junctions-methods junctions junctions,GAlignments-method
> ###   junctions,GAlignmentPairs-method junctions,GAlignmentsList-method
> ###   NATURAL_INTRON_MOTIFS summarizeJunctions readTopHatJunctions
> ###   readSTARJunctions
> ### Keywords: methods manip
> 
> ### ** Examples
> 
> library(RNAseqData.HNRNPC.bam.chr14)
> bamfile <- RNAseqData.HNRNPC.bam.chr14_BAMFILES[1]
> 
> ## ---------------------------------------------------------------------
> ## A. junctions()
> ## ---------------------------------------------------------------------
> 
> gal <- readGAlignments(bamfile)
> table(njunc(gal))  # some alignments have 3 junctions!

     0      1      2      3 
607197 189110   4153     24 
> juncs <- junctions(gal)
> juncs
GRangesList object of length 800484:
[[1]]
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 93 sequences from an unspecified genome

[[2]]
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 93 sequences from an unspecified genome

[[3]]
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 93 sequences from an unspecified genome

...
<800481 more elements>
> 
> stopifnot(identical(unname(elementNROWS(juncs)), njunc(gal)))
> 
> galp <- readGAlignmentPairs(bamfile)
Warning in .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode,  :
    376 alignments with ambiguous pairing were dumped.
    Use 'getDumpedAlignments()' to retrieve them from the dump environment.
> juncs <- junctions(galp)
> juncs
GRangesList object of length 400054:
[[1]]
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 93 sequences from an unspecified genome

[[2]]
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 93 sequences from an unspecified genome

[[3]]
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 93 sequences from an unspecified genome

...
<400051 more elements>
> 
> stopifnot(identical(unname(elementNROWS(juncs)), njunc(galp)))
> 
> ## ---------------------------------------------------------------------
> ## B. summarizeJunctions()
> ## ---------------------------------------------------------------------
> 
> ## By default, only the "score", "plus_score", and "minus_score"
> ## metadata columns are returned:
> junc_summary <- summarizeJunctions(gal)
> junc_summary
GRanges object with 4635 ranges and 3 metadata columns:
         seqnames              ranges strand |     score plus_score minus_score
            <Rle>           <IRanges>  <Rle> | <integer>  <integer>   <integer>
     [1]    chr14   19650127-19652243      * |         4          2           2
     [2]    chr14   19650127-19653624      * |         1          1           0
     [3]    chr14   19652355-19653624      * |         8          7           1
     [4]    chr14   19652355-19653657      * |         1          1           0
     [5]    chr14   19653773-19653892      * |         9          5           4
     ...      ...                 ...    ... .       ...        ...         ...
  [4631]    chr14 106912703-106922227      * |         1          0           1
  [4632]    chr14 106938165-106938301      * |        10          2           8
  [4633]    chr14 106938645-106944774      * |        24          7          17
  [4634]    chr14 106944969-106950170      * |         7          6           1
  [4635]    chr14 106950323-106960260      * |         1          1           0
  -------
  seqinfo: 93 sequences from an unspecified genome
> 
> ## The "score" metadata column reports the total number of alignments
> ## crossing each junction, i.e., that have the junction encoded in their
> ## CIGAR:
> median(mcols(junc_summary)$score)
[1] 12
> 
> ## The "plus_score" and "minus_score" metadata columns report the
> ## strand-specific number of alignments crossing each junction:
> stopifnot(identical(mcols(junc_summary)$score,
+                     mcols(junc_summary)$plus_score +
+                     mcols(junc_summary)$minus_score))
> 
> ## If 'with.revmap' is TRUE, the "revmap" metadata column is added to
> ## the output. This metadata column is an IntegerList object represen-
> ## ting the mapping from each element in the ouput (i.e. a junction) to
> ## the corresponding elements in the input 'x'. Here we're going to use
> ## this to compute a 'score2' for each junction. We obtain this score
> ## by summing the mapping qualities of the alignments crossing the
> ## junction:
> gal <- readGAlignments(bamfile, param=ScanBamParam(what="mapq"))
> junc_summary <- summarizeJunctions(gal, with.revmap=TRUE)
> junc_score2 <- sum(extractList(mcols(gal)$mapq,
+                                mcols(junc_summary)$revmap))
> mcols(junc_summary)$score2 <- junc_score2
> 
> ## If the name of the reference genome is specified thru the 'genome'
> ## argument (in which case the corresponding BSgenome data package needs
> ## to be installed), then summarizeJunctions() returns the intron motif
> ## and strand for each junction.
> ## Since the reads in RNAseqData.HNRNPC.bam.chr14 were aligned to
> ## the hg19 genome, the following requires that you have
> ## BSgenome.Hsapiens.UCSC.hg19 installed:
> junc_summary <- summarizeJunctions(gal, with.revmap=TRUE, genome="hg19")
> mcols(junc_summary)$score2 <- junc_score2  # putting 'score2' back
> 
> ## The "intron_motif" metadata column is a factor whose levels are the
> ## 5 natural intron motifs stored in predefined character vector
> ## 'NATURAL_INTRON_MOTIFS':
> table(mcols(junc_summary)$intron_motif)

GT-AG GC-AG AT-AC AT-AA AT-AG 
 4543    74    18     0     0 
> 
> ## ---------------------------------------------------------------------
> ## C. STRANDED RNA-seq PROTOCOL
> ## ---------------------------------------------------------------------
> 
> ## Here is a simple test for checking whether the RNA-seq protocol was
> ## stranded or not:
> strandedTest <- function(plus_score, minus_score)
+     (sum(plus_score ^ 2) + sum(minus_score ^ 2)) /
+         sum((plus_score + minus_score) ^ 2)
> 
> ## The result of this test is guaranteed to be >= 0.5 and <= 1.
> ## If, for each junction, the strand of the crossing alignments looks
> ## random (i.e. "plus_score" and "minus_score" are close), then
> ## strandedTest() will return a value close to 0.5. If it doesn't look
> ## random (i.e. for each junction, one of "plus_score" and "minus_score"
> ## is much bigger than the other), then strandedTest() will return a
> ## value close to 1.
> 
> ## If the reads are single-end, the test is meaningful when applied
> ## directly on 'junc_summary'. However, for the test to be meaningful
> ## on paired-end reads, it needs to be applied on the first and last
> ## alignments separately:
> junc_summary1 <- summarizeJunctions(first(galp))
> junc_summary2 <- summarizeJunctions(last(galp))
> strandedTest(mcols(junc_summary1)$plus_score,
+              mcols(junc_summary1)$minus_score)
[1] 0.5493679
> strandedTest(mcols(junc_summary2)$plus_score,
+              mcols(junc_summary2)$minus_score)
[1] 0.5469448
> ## Both values are close to 0.5 which suggests that the RNA-seq protocol
> ## used for this experiment was not stranded.
> 
> ## ---------------------------------------------------------------------
> ## D. UTILITIES FOR IMPORTING THE JUNCTION FILE GENERATED BY SOME
> ##    ALIGNERS
> ## ---------------------------------------------------------------------
> 
> ## The TopHat aligner generates a junctions.bed file where it reports
> ## all the junctions satisfying some "quality" criteria (see the TopHat
> ## manual at http://tophat.cbcb.umd.edu/manual.shtml for more
> ## information). This file can be loaded with readTopHatJunctions():
> runname <- names(RNAseqData.HNRNPC.bam.chr14_BAMFILES)[1]
> junctions_file <- system.file("extdata", "tophat2_out", runname,
+                               "junctions.bed",
+                               package="RNAseqData.HNRNPC.bam.chr14")
> th_junctions <- readTopHatJunctions(junctions_file)
Error in writeLines(text, con) : 
  Error writing to connection:  No space left on device
Calls: readTopHatJunctions ... lapply -> lapply -> FUN -> import -> import -> writeLines
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
coordinate-mapping-methods 5.55  0.082   5.642
* checking for unstated dependencies in ‘tests’ ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking tests ...Fatal error: cannot create 'R_TempDir'
 ERROR
* checking for unstated dependencies in vignettes ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
Fatal error: cannot create 'R_TempDir'

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
Re-running with no redirection of stdout/stderr.
Fatal error: cannot create 'R_TempDir'
* DONE

Status: 4 ERRORs, 2 WARNINGs, 7 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GenomicAlignments.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL GenomicAlignments
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘GenomicAlignments’ ...
** this is package ‘GenomicAlignments’ version ‘1.43.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c cigar_utils.c -o cigar_utils.o
In file included from /home/rapidbuild/bbs-3.21-bioc-rapid/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/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #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/rapidbuild/bbs-3.21-bioc-rapid/R/include/Rinternals.h:388:36: note: in definition of macro ‘PROTECT’
  388 | #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/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -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/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -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/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
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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)