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INSTALL report for Biostrings on malbec1

This page was generated on 2021-05-06 12:27:00 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the Biostrings package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 187/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.58.0  (landing page)
H. Pagès
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Biostrings
Branch: RELEASE_3_12
Last Commit: 0ec1a54
Last Changed Date: 2020-10-27 10:23:25 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Biostrings
Version: 2.58.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Biostrings
StartedAt: 2021-05-05 16:09:59 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 16:10:35 -0400 (Wed, 05 May 2021)
EllapsedTime: 36.4 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Biostrings
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c BAB_class.c -o BAB_class.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c BitMatrix.c -o BitMatrix.o
BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function]
 static void BitMatrix_print(BitMatrix *bitmat)
             ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c MIndex_class.c -o MIndex_class.o
MIndex_class.c: In function ‘SparseMIndex_endIndex’:
MIndex_class.c:184:20: warning: unused variable ‘poffsets_order’ [-Wunused-variable]
  IntAE *poffsets, *poffsets_order;
                    ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c XStringSet_class.c -o XStringSet_class.o
XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’:
XStringSet_class.c:124:3: warning: ‘lkup_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt,
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     INTEGER(start)[i], lkup0, lkup_len);
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c XString_class.c -o XString_class.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c align_needwunsQS.c -o align_needwunsQS.o
align_needwunsQS.c: In function ‘align_needwunsQS’:
align_needwunsQS.c:155:22: warning: ‘sc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  INTEGER(ans_elt)[0] = score;
  ~~~~~~~~~~~~~~~~~~~~^~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:254:14: warning: ‘indelWidthSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     jPattern += indelWidthSubject;
     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:235:42: warning: ‘indelStartSubject’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
                                       ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:225:26: warning: ‘indelWidthPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
                          ^~~~~~~~~~~~~~~~~
align_utils.c:236:50: warning: ‘indelStartPattern’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
                                        ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c find_palindromes.c -o find_palindromes.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c inject_code.c -o inject_code.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c letter_frequency.c -o letter_frequency.o
letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’:
letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable]
   int x_width, y_width, x_length, *ans_mat, i, x_pos;
                                                ^~~~~
letter_frequency.c:956:13: warning: unused variable ‘ans_dimnames’ [-Wunused-variable]
   SEXP ans, ans_dimnames;
             ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_PWM.c -o match_PWM.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pattern.c -o match_pattern.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pattern_indels.c -o match_pattern_indels.o
match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function]
 static void test_match_pattern_indels(const char *p, const char *s,
             ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pdict.c -o match_pdict.o
match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’:
match_pdict.c:419:12: warning: ‘ans_col’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    ans_col += tb_length;
    ~~~~~~~~^~~~~~~~~~~~
match_pdict.c:392:58: note: ‘ans_col’ was declared here
  int tb_length, S_length, collapse0, i, j, match_count, *ans_col;
                                                          ^~~~~~~
match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’:
match_pdict.c:470:13: warning: ‘ans_elt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     ans_elt += P_length;
     ~~~~~~~~^~~~~~~~~~~
match_pdict.c:441:57: note: ‘ans_elt’ was declared here
  int P_length, S_length, collapse0, i, j, match_count, *ans_elt;
                                                         ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
match_pdict_ACtree2.c: In function ‘split_and_move_pointers’:
match_pdict_ACtree2.c:1031:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^~~~~
match_pdict_ACtree2.c: In function ‘merge_pointers’:
match_pdict_ACtree2.c:1076:10: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable]
  ACnode *node0, *node1, *node2;
          ^~~~~
At top level:
match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function]
 static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes)
                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function]
 static void debug_node_counting_functions(int maxdepth)
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pdict_Twobit.c -o match_pdict_Twobit.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from match_pdict_Twobit.c:10:
match_pdict_Twobit.c: In function ‘build_Twobit’:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:984:20: warning: ‘twobit_sign2pos’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^~~~~~~~~~
match_pdict_Twobit.c:110:12: note: ‘twobit_sign2pos’ was declared here
  SEXP ans, twobit_sign2pos;
            ^~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_pdict_utils.c -o match_pdict_utils.o
match_pdict_utils.c: In function ‘match_ppheadtail0’:
match_pdict_utils.c:652:49: warning: unused variable ‘ncol’ [-Wunused-variable]
  int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol;
                                                 ^~~~
match_pdict_utils.c: In function ‘match_ppheadtail’:
match_pdict_utils.c:712:6: warning: unused variable ‘nelt’ [-Wunused-variable]
  int nelt, nkey0, nkey1, nkey2, i, key;
      ^~~~
match_pdict_utils.c: In function ‘_match_pdict_all_flanks’:
match_pdict_utils.c:819:44: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^~~~~~~~~~~~
match_pdict_utils.c:819:27: warning: unused variable ‘total_NFC’ [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^~~~~~~~~
match_pdict_utils.c:818:33: warning: unused variable ‘NFC’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                                 ^~~
match_pdict_utils.c:818:26: warning: unused variable ‘nloci’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                          ^~~~~
match_pdict_utils.c:818:20: warning: unused variable ‘ndup’ [-Wunused-variable]
  unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons
                    ^~~~
At top level:
match_pdict_utils.c:819:27: warning: ‘total_NFC’ defined but not used [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                           ^~~~~~~~~
match_pdict_utils.c:819:44: warning: ‘subtotal_NFC’ defined but not used [-Wunused-variable]
  static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL;
                                            ^~~~~~~~~~~~
match_pdict_utils.c:260:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function]
 static void match_headtail_by_loc(const HeadTail *headtail,
             ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c match_reporting.c -o match_reporting.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c read_fasta_files.c -o read_fasta_files.o
read_fasta_files.c: In function ‘read_fasta_files’:
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+64)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return loader_ext;
         ^~~~~~~~~~
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+72)’ may be used uninitialized in this function [-Wmaybe-uninitialized]
read_fasta_files.c: In function ‘read_fasta_blocks’:
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+64)’ is used uninitialized in this function [-Wuninitialized]
  return loader_ext;
         ^~~~~~~~~~
read_fasta_files.c:186:9: warning: ‘*((void *)&loader_ext+72)’ is used uninitialized in this function [-Wuninitialized]
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c read_fastq_files.c -o read_fastq_files.o
read_fastq_files.c: In function ‘parse_FASTQ_file’:
read_fastq_files.c:392:7: warning: ‘dont_load’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (dont_load || loader->new_empty_seq_hook == NULL)
       ^
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c replace_letter_at.c -o replace_letter_at.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c translate.c -o translate.o
translate.c: In function ‘DNAStringSet_translate’:
translate.c:110:8: warning: ‘if_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_ambig == TRANSLATE_ERROR) {
        ^
translate.c:136:29: note: ‘if_ambig0’ was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
                             ^~~~~~~~~
translate.c:106:8: warning: ‘if_non_ambig0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (if_non_ambig == TRANSLATE_TO_X)
        ^
translate.c:136:14: note: ‘if_non_ambig0’ was declared here
  int ncodes, if_non_ambig0, if_ambig0, ans_length, i, errcode;
              ^~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
utils.c: In function ‘_get_twobit_signature’:
utils.c:157:9: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  return twobit_sign;
         ^~~~~~~~~~~
utils.c: In function ‘_get_twobit_signature_at’:
utils.c:164:12: warning: ‘twobit_sign’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  int i, j, twobit_sign;
            ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/XVector/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c xscat.c -o xscat.o
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XString_xscat’:
/home/biocbuild/bbs-3.12-bioc/R/include/Rdefines.h:98:21: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_RAW(n)  Rf_allocVector(RAWSXP,n)
                     ^~~~~~~~~~~~~~
xscat.c:18:13: note: ‘ans_length’ was declared here
  int nargs, ans_length, tag_offset, j;
             ^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:984:20: warning: ‘ans_classname’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^~~~~~~~~~
xscat.c:20:14: note: ‘ans_classname’ was declared here
  const char *ans_classname;
              ^~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
xscat.c: In function ‘XStringSet_xscat’:
/home/biocbuild/bbs-3.12-bioc/R/include/Rdefines.h:92:25: warning: ‘ans_length’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define NEW_INTEGER(n)  Rf_allocVector(INTSXP,n)
                         ^~~~~~~~~~~~~~
xscat.c:66:32: note: ‘ans_length’ was declared here
  int nargs, *arg_lengths, *ii, ans_length, i, j, *width;
                                ^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/IRanges/include/IRanges_defines.h:18,
                 from ../inst/include/Biostrings_defines.h:18,
                 from Biostrings.h:1,
                 from xscat.c:1:
/home/biocbuild/bbs-3.12-bioc/R/include/Rinternals.h:984:20: warning: ‘ans_element_type’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PROTECT(s) Rf_protect(s)
                    ^~~~~~~~~~
xscat.c:68:14: note: ‘ans_element_type’ was declared here
  const char *ans_element_type;
              ^~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’
** 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 (Biostrings)