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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cigarillo.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cigarillo_0.99.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cigarillo.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘cigarillo/DESCRIPTION’ ... OK
* this is package ‘cigarillo’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘cigarillo’ 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 ... OK
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  project_sequences.Rd: XStringSet
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
project_sequences       12.220  0.572  12.794
map_ref_ranges_to_query  9.432  0.002   9.434
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/cigarillo.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL cigarillo
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘cigarillo’ ...
** this is package ‘cigarillo’ version ‘0.99.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/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 -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_cigarillo.c -o R_init_cigarillo.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/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 -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c cigar_extent.c -o cigar_extent.o
cigar_extent.c: In function ‘C_cigar_extent’:
cigar_extent.c:44:29: warning: ‘flags_elt’ may be used uninitialized [-Wmaybe-uninitialized]
   44 |                         if (*flags_elt == NA_INTEGER) {
      |                             ^~~~~~~~~~
cigar_extent.c:34:20: note: ‘flags_elt’ was declared here
   34 |         const int *flags_elt;
      |                    ^~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c cigar_ops_visibility.c -o cigar_ops_visibility.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c cigars_as_ranges.c -o cigars_as_ranges.o
cigars_as_ranges.c: In function ‘C_cigars_as_ranges’:
cigars_as_ranges.c:327:48: warning: ‘range_buf2’ may be used uninitialized [-Wmaybe-uninitialized]
  327 |                         range_buf1 = range_buf2->elts[*f_p - 1];
      |                                      ~~~~~~~~~~^~~~~~
cigars_as_ranges.c:260:22: note: ‘range_buf2’ was declared here
  260 |         IntPairAEAE *range_buf2;
      |                      ^~~~~~~~~~
cigars_as_ranges.c:295:29: warning: ‘flags_p’ may be used uninitialized [-Wmaybe-uninitialized]
  295 |                         if (*flags_p == NA_INTEGER) {
      |                             ^~~~~~~~
cigars_as_ranges.c:250:20: note: ‘flags_p’ was declared here
  250 |         const int *flags_p;
      |                    ^~~~~~~
cigars_as_ranges.c:344:38: warning: ‘breakpoints’ may be used uninitialized [-Wmaybe-uninitialized]
  344 |                         *(breakpoints++) = IntPairAE_get_nelt(range_buf1);
      |                          ~~~~~~~~~~~~^~~
cigars_as_ranges.c:262:14: note: ‘breakpoints’ was declared here
  262 |         int *breakpoints;
      |              ^~~~~~~~~~~
cigars_as_ranges.c:325:29: warning: ‘f_p’ may be used uninitialized [-Wmaybe-uninitialized]
  325 |                         if (*f_p == NA_INTEGER)
      |                             ^~~~
cigars_as_ranges.c:264:20: note: ‘f_p’ was declared here
  264 |         const int *f_p;
      |                    ^~~
In function ‘parse_cigar_ranges’,
    inlined from ‘C_cigars_as_ranges’ at cigars_as_ranges.c:329:24:
cigars_as_ranges.c:142:25: warning: ‘range_buf1’ may be used uninitialized [-Wmaybe-uninitialized]
  142 |         int buf_nelt0 = IntPairAE_get_nelt(range_buf);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigars_as_ranges.c: In function ‘C_cigars_as_ranges’:
cigars_as_ranges.c:259:20: note: ‘range_buf1’ was declared here
  259 |         IntPairAE *range_buf1;
      |                    ^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.22-bioc/R/include/Rdefines.h:41,
                 from cigars_as_ranges.h:4,
                 from cigars_as_ranges.c:1:
In function ‘make_CompressedIRangesList’,
    inlined from ‘C_cigars_as_ranges’ at cigars_as_ranges.c:352:3:
/home/biocbuild/bbs-3.22-bioc/R/include/Rinternals.h:388:25: warning: ‘ans_breakpoints’ may be used uninitialized [-Wmaybe-uninitialized]
  388 | #define PROTECT(s)      Rf_protect(s)
      |                         ^~~~~~~~~~~~~
cigars_as_ranges.c:204:17: note: in expansion of macro ‘PROTECT’
  204 |                 PROTECT(new_PartitioningByEnd("PartitioningByEnd",
      |                 ^~~~~~~
cigars_as_ranges.c: In function ‘C_cigars_as_ranges’:
cigars_as_ranges.c:261:14: note: ‘ans_breakpoints’ was declared here
  261 |         SEXP ans_breakpoints;
      |              ^~~~~~~~~~~~~~~
In function ‘make_list_of_IRanges’,
    inlined from ‘C_cigars_as_ranges’ at cigars_as_ranges.c:350:10:
/home/biocbuild/bbs-3.22-bioc/R/include/Rdefines.h:146:33: warning: ‘f_levels’ may be used uninitialized [-Wmaybe-uninitialized]
  146 | #define SET_NAMES(x, n)         Rf_setAttrib(x, R_NamesSymbol, n)
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cigars_as_ranges.c:176:9: note: in expansion of macro ‘SET_NAMES’
  176 |         SET_NAMES(ans, names);
      |         ^~~~~~~~~
cigars_as_ranges.c: In function ‘C_cigars_as_ranges’:
cigars_as_ranges.c:263:14: note: ‘f_levels’ was declared here
  263 |         SEXP f_levels;
      |              ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c explode_cigars.c -o explode_cigars.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c map_ref_ranges_to_query.c -o map_ref_ranges_to_query.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c project_positions.c -o project_positions.o
project_positions.c: In function ‘_to_ref’:
project_positions.c:67:6: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized]
   67 |   if (n == 0)
      |      ^
project_positions.c:20:7: note: ‘n’ was declared here
   20 |   int n, offset = 0, OPL, query_consumed = 0;
      |       ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c tabulate_cigar_ops.c -o tabulate_cigar_ops.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c trim_cigars.c -o trim_cigars.o
In function ‘trim_along_ref’,
    inlined from ‘C_trim_cigars_along_ref’ at trim_cigars.c:178:24:
trim_cigars.c:130:12: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized]
  130 |         if (Roffset < Loffset) {
      |            ^
trim_cigars.c: In function ‘C_trim_cigars_along_ref’:
trim_cigars.c:118:13: note: ‘Loffset’ was declared here
  118 |         int Loffset;
      |             ^~~~~~~
In function ‘trim_along_ref’,
    inlined from ‘C_trim_cigars_along_ref’ at trim_cigars.c:178:24:
trim_cigars.c:130:12: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized]
  130 |         if (Roffset < Loffset) {
      |            ^
trim_cigars.c: In function ‘C_trim_cigars_along_ref’:
trim_cigars.c:125:13: note: ‘Roffset’ was declared here
  125 |         int Roffset;
      |             ^~~~~~~
In function ‘trim_along_query’,
    inlined from ‘C_trim_cigars_along_query’ at trim_cigars.c:364:24:
trim_cigars.c:311:12: warning: ‘Loffset’ may be used uninitialized [-Wmaybe-uninitialized]
  311 |         if (Roffset < Loffset) {
      |            ^
trim_cigars.c: In function ‘C_trim_cigars_along_query’:
trim_cigars.c:299:13: note: ‘Loffset’ was declared here
  299 |         int Loffset;
      |             ^~~~~~~
In function ‘trim_along_query’,
    inlined from ‘C_trim_cigars_along_query’ at trim_cigars.c:364:24:
trim_cigars.c:311:12: warning: ‘Roffset’ may be used uninitialized [-Wmaybe-uninitialized]
  311 |         if (Roffset < Loffset) {
      |            ^
trim_cigars.c: In function ‘C_trim_cigars_along_query’:
trim_cigars.c:306:13: note: ‘Roffset’ was declared here
  306 |         int Roffset;
      |             ^~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o cigarillo.so IRanges_stubs.o R_init_cigarillo.o S4Vectors_stubs.o cigar_extent.o cigar_ops_visibility.o cigars_as_ranges.o explode_cigars.o map_ref_ranges_to_query.o project_positions.o tabulate_cigar_ops.o trim_cigars.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-cigarillo/00new/cigarillo/libs
** R
** 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 (cigarillo)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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
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Type 'q()' to quit R.

> library(testthat)
> library(cigarillo)
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Biostrings
Loading required package: XVector
Loading required package: Seqinfo

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_check("cigarillo")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 557 ]
> 
> proc.time()
   user  system elapsed 
  9.720   0.537  10.254