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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:triplex.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings triplex_1.49.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/triplex.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'triplex/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'triplex' version '1.49.0'
* 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 whether package 'triplex' can be installed ... WARNING
Found the following significant warnings:
  search_interface.c:371:84: warning: pointer used after 'free' [-Wuse-after-free]
  Warning: replacing previous import 'grid::pattern' by 'Biostrings::pattern' when loading 'triplex'
See 'F:/biocbuild/bbs-3.22-bioc/meat/triplex.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'triplex' for: 'type'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: 'IRanges:::new_Views'
  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 ... NOTE
countBend: no visible global function definition for 'optimize'
drawBase: no visible global function definition for 'rgl.triangles'
join: no visible global function definition for 'rgl.quads'
joinRect: no visible global function definition for 'rgl.quads'
triplex.3D: no visible global function definition for
  'installed.packages'
triplex.3D: no visible global function definition for 'type'
triplex.3D: no visible global function definition for 'nlm'
triplex.3D: no visible global function definition for 'rgl.bg'
triplex.3D: no visible global function definition for 'rgl.spheres'
triplex.diagram: no visible global function definition for 'type'
triplex.input: no visible global function definition for 'type'
coerce,TriplexViews-DNAStringSet: no visible global function definition
  for 'type'
coerce,TriplexViews-GRanges: no visible global function definition for
  'type'
Undefined global functions or variables:
  installed.packages nlm optimize rgl.bg rgl.quads rgl.spheres
  rgl.triangles type
Consider adding
  importFrom("stats", "nlm", "optimize")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) TriplexViews-class.Rd:68-71: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:72-75: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:76-80: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:81-84: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:85-88: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:89-92: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:93-96: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:97-100: \item in \describe must have non-empty label
checkRd: (5) TriplexViews-class.Rd:101-104: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  TriplexViews-class.Rd: DNAString, XStringViews
  triplex-package.Rd: DNAString
  triplex.3D.Rd: DNAStringSet
  triplex.alignment.Rd: DNAStringSet
  triplex.diagram.Rd: DNAStringSet
  triplex.search.Rd: DNAString, XStringViews
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 for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/triplex/libs/x64/triplex.dll':
  Found '_exit', possibly from '_exit' (C)
  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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/triplex.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL triplex
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'triplex' ...
** this is package 'triplex' version '1.49.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c R_init_triplex.c -o R_init_triplex.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c XVector_stubs.c -o XVector_stubs.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c align.c -o align.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c align_interface.c -o align_interface.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c dl_list.c -o dl_list.o
dl_list.c: In function 'dl_list_merge_sort':
dl_list.c:307:19: warning: 'act_start' may be used uninitialized [-Wmaybe-uninitialized]
  307 |                if ((act_start < min_start) ||
      |                   ^
dl_list.c:283:41: note: 'act_start' was declared here
  283 |    int i, min_list, min_start, min_end, act_start, act_end, items = 0;
      |                                         ^~~~~~~~~
dl_list.c:308:46: warning: 'act_end' may be used uninitialized [-Wmaybe-uninitialized]
  308 |                    ((act_start == min_start) && (act_end < min_end))){
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
dl_list.c:283:52: note: 'act_end' was declared here
  283 |    int i, min_list, min_start, min_end, act_start, act_end, items = 0;
      |                                                    ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c interval.c -o interval.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c libtriplex.c -o libtriplex.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c progress.c -o progress.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c search.c -o search.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/S4Vectors/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/Biostrings/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c search_interface.c -o search_interface.o
search_interface.c: In function 'decode_DNAString':
search_interface.c:371:84: warning: pointer used after 'free' [-Wuse-after-free]
  371 |                         error("Unsupported symbol '%c' in input sequence.", dna.seq[i]);
      |                                                                                    ^
search_interface.c:370:25: note: call to 'free' here
  370 |                         free(dna.seq);
      |                         ^~~~~~~~~~~~~
gcc -shared -s -static-libgcc -o triplex.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o XVector_stubs.o align.o align_interface.o dl_list.o interval.o libtriplex.o progress.o search.o search_interface.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-triplex/00new/triplex/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'grid::pattern' by 'Biostrings::pattern' when loading 'triplex'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'grid::pattern' by 'Biostrings::pattern' when loading 'triplex'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'grid::pattern' by 'Biostrings::pattern' when loading 'triplex'
** testing if installed package keeps a record of temporary installation path
* DONE (triplex)