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INSTALL report for Biostrings on malbec1

This page was generated on 2019-04-16 11:47:53 -0400 (Tue, 16 Apr 2019).

Package 159/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biostrings 2.50.2
H. Pag├Ęs
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Biostrings
Branch: RELEASE_3_8
Last Commit: 025e734
Last Changed Date: 2019-01-03 09:57:07 -0400 (Thu, 03 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64 [ OK ] OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Biostrings
Version: 2.50.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Biostrings
StartedAt: 2019-04-15 18:05:06 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 18:05:45 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 38.4 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Biostrings
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘Biostrings’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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,
   ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c gtestsim.c -o gtestsim.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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;
          ^
match_pdict_ACtree2.c: At top level:
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)
             ^
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)
                     ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/Rinternals.h:809:20: 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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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
                    ^
match_pdict_utils.c: At top level:
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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c matchprobes.c -o matchprobes.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c read_fasta_files.c -o read_fasta_files.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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:310:8: warning: ‘seq_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (data.length != seq_len) {
        ^
read_fastq_files.c:309:7: warning: ‘load_rec’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    if (load_rec) {
       ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c replaceAt.c -o replaceAt.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c strutils.c -o strutils.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/Rinternals.h:809:20: 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-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18:0,
                 from /home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/include/Rdefines.h:40:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include/S4Vectors_defines.h:18,
                 from /home/biocbuild/bbs-3.8-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-3.8-bioc/R/include/Rinternals.h:809:20: 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-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/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
* DONE (Biostrings)