##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:XVector.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings XVector_0.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/XVector.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 ‘XVector/DESCRIPTION’ ... OK
* this is package ‘XVector’ version ‘0.46.0’
* 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 ‘XVector’ 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 DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’
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 ... 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 whether startup messages can be suppressed ... 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 ... WARNING
Missing link or links in Rd file 'XRawList-comparison.Rd':
  ‘[IRanges]{Ranges-comparison}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘RdaCollection’ ‘RdsCollection’ ‘open_input_files’ ‘rdaPath’
Undocumented S4 classes:
  ‘RdaCollection’ ‘RdsCollection’
Undocumented S4 methods:
  generic '[[' and siglist 'RdaCollection'
  generic 'coerce' and siglist 'XVector,Rle'
  generic 'extractList' and siglist 'XVector,IntegerRanges'
  generic 'extractROWS' and siglist 'RdsCollection,ANY'
  generic 'extractROWS' and siglist 'XVector,ANY'
  generic 'extractROWS' and siglist 'XVectorList,ANY'
  generic 'getListElement' and siglist 'RdsCollection'
  generic 'getListElement' and siglist 'XVectorList'
  generic 'length' and siglist 'RdaCollection'
  generic 'names' and siglist 'RdaCollection'
  generic 'names' and siglist 'RdsCollection'
  generic 'parallel_slot_names' and siglist 'RdsCollection'
  generic 'path' and siglist 'RdsCollection'
  generic 'rdaPath' and siglist 'RdaCollection'
  generic 'relist' and siglist 'XVector,PartitioningByEnd'
  generic 'relistToClass' and siglist 'XVector'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/XVector.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL XVector
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘XVector’ ...
** 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 Ocopy_byteblocks.c -o Ocopy_byteblocks.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 RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function ‘RDS_extract_subarray’:
RDS_random_access.c:796:25: warning: unused variable ‘ans’ [-Wunused-variable]
  796 |         SEXP subscript, ans;
      |                         ^~~
RDS_random_access.c:793:18: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable]
  793 |         SEXPTYPE x_type;
      |                  ^~~~~~
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_XVector.c -o R_init_XVector.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 SharedDouble_class.c -o SharedDouble_class.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 SharedInteger_class.c -o SharedInteger_class.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 SharedRaw_class.c -o SharedRaw_class.o
SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’:
SharedRaw_class.c:396:20: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable]
  396 |         SEXP dest, src_tag;
      |                    ^~~~~~~
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 SharedVector_class.c -o SharedVector_class.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 XDouble_class.c -o XDouble_class.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 XInteger_class.c -o XInteger_class.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 XRawList_comparison.c -o XRawList_comparison.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 XRaw_class.c -o XRaw_class.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 XVectorList_class.c -o XVectorList_class.o
XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’:
XVectorList_class.c:459:17: warning: ‘lkup_length’ may be used uninitialized [-Wmaybe-uninitialized]
  459 |                 _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1,
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  460 |                         (char *) dest.ptr, dest.length,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  461 |                         src->elts, CharAE_get_nelt(src),
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  462 |                         lkup0, lkup_length);
      |                         ~~~~~~~~~~~~~~~~~~~
XVectorList_class.c:434:13: note: ‘lkup_length’ was declared here
  434 |         int lkup_length, nelt, i;
      |             ^~~~~~~~~~~
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 XVector_class.c -o XVector_class.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 io_utils.c -o io_utils.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 slice_methods.c -o slice_methods.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 vector_copy.c -o vector_copy.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 view_summarization_methods.c -o view_summarization_methods.o
view_summarization_methods.c: In function ‘get_which_min_from_Ints_holder’:
view_summarization_methods.c:219:45: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized]
  219 |                 if (which_min == NA_INTEGER || x < cur_min) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:208:19: note: ‘cur_min’ was declared here
  208 |         int xlen, cur_min, which_min, i, x;
      |                   ^~~~~~~
view_summarization_methods.c: In function ‘get_which_min_from_Doubles_holder’:
view_summarization_methods.c:246:45: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized]
  246 |                 if (which_min == NA_INTEGER || x < cur_min) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:235:16: note: ‘cur_min’ was declared here
  235 |         double cur_min, x;
      |                ^~~~~~~
view_summarization_methods.c: In function ‘get_which_max_from_Ints_holder’:
view_summarization_methods.c:269:45: warning: ‘cur_max’ may be used uninitialized [-Wmaybe-uninitialized]
  269 |                 if (which_max == NA_INTEGER || x > cur_max) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:258:19: note: ‘cur_max’ was declared here
  258 |         int xlen, cur_max, which_max, i, x;
      |                   ^~~~~~~
view_summarization_methods.c: In function ‘get_which_max_from_Doubles_holder’:
view_summarization_methods.c:296:45: warning: ‘cur_max’ may be used uninitialized [-Wmaybe-uninitialized]
  296 |                 if (which_max == NA_INTEGER || x > cur_max) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
view_summarization_methods.c:285:16: note: ‘cur_max’ was declared here
  285 |         double cur_max, x;
      |                ^~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -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-XVector/00new/XVector/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (XVector)

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("XVector") || stop("unable to load XVector package")
Loading required package: XVector
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, saveRDS, 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
[1] TRUE
> XVector:::.test()


RUNIT TEST PROTOCOL -- Fri Nov  1 10:09:33 2024 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
XVector RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.926   0.157   2.897