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### Running command:
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###   /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL S4Vectors
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* installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c AEbufs.c -o AEbufs.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Hits_class.c -o Hits_class.o
In file included from /home/hpages/bbs-3.18-bioc/R/include/Rdefines.h:41,
                 from ../inst/include/S4Vectors_defines.h:18,
                 from S4Vectors.h:1,
                 from Hits_class.c:4:
/home/hpages/bbs-3.18-bioc/R/include/Rinternals.h: In function ‘Hits_new’:
/home/hpages/bbs-3.18-bioc/R/include/Rinternals.h:886:33: warning: ‘revmap’ may be used uninitialized [-Wmaybe-uninitialized]
  886 | #define defineVar               Rf_defineVar
      |                                 ^~~~~~~~~~~~
Hits_class.c:216:19: note: ‘revmap’ was declared here
  216 |         SEXP ans, revmap, symbol;
      |                   ^~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c LLint_class.c -o LLint_class.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c List_class.c -o List_class.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Rle_class.c -o Rle_class.o
Rle_class.c: In function ‘fill_integer_runs’:
Rle_class.c:278:38: warning: ‘val_out’ may be used uninitialized [-Wmaybe-uninitialized]
  278 |                 values_out[nrun_out] = val_out;
      |                 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
Rle_class.c:245:21: note: ‘val_out’ was declared here
  245 |         int val_in, val_out;
      |                     ^~~~~~~
In function ‘fill_numeric_runs’,
    inlined from ‘_construct_numeric_Rle’ at Rle_class.c:765:2:
Rle_class.c:377:38: warning: ‘val_out’ may be used uninitialized [-Wmaybe-uninitialized]
  377 |                 values_out[nrun_out] = val_out;
      |                 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
Rle_class.c: In function ‘_construct_numeric_Rle’:
Rle_class.c:344:24: note: ‘val_out’ was declared here
  344 |         double val_in, val_out;
      |                        ^~~~~~~
In function ‘fill_character_runs’,
    inlined from ‘_construct_character_Rle’ at Rle_class.c:813:2:
Rle_class.c:575:17: warning: ‘val_out’ may be used uninitialized [-Wmaybe-uninitialized]
  575 |                 SET_STRING_ELT(values_out, nrun_out, val_out);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Rle_class.c: In function ‘_construct_character_Rle’:
Rle_class.c:541:22: note: ‘val_out’ was declared here
  541 |         SEXP val_in, val_out;
      |                      ^~~~~~~
In function ‘fill_raw_runs’,
    inlined from ‘_construct_raw_Rle’ at Rle_class.c:838:2:
Rle_class.c:671:38: warning: ‘val_out’ may be used uninitialized [-Wmaybe-uninitialized]
  671 |                 values_out[nrun_out] = val_out;
      |                 ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
Rle_class.c: In function ‘_construct_raw_Rle’:
Rle_class.c:638:23: note: ‘val_out’ was declared here
  638 |         Rbyte val_in, val_out;
      |                       ^~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c Rle_utils.c -o Rle_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c anyMissing.c -o anyMissing.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c character_utils.c -o character_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c eval_utils.c -o eval_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c hash_utils.c -o hash_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c integer_utils.c -o integer_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c logical_utils.c -o logical_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c raw_utils.c -o raw_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c safe_arithm.c -o safe_arithm.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function]
  263 | static void sort_uchar_array(unsigned char *x, int nelt, int desc)
      |             ^~~~~~~~~~~~~~~~
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c vector_utils.c -o vector_utils.o
gcc -shared -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o
installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/00LOCK-S4Vectors/00new/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List”
Creating a new generic function for ‘unname’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame”
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table”
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
** 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 (S4Vectors)