Merge pull request #1032 from genometools/clang-build-fixes

Clang build fixes
genometools · Oct 7, 2023 · 8cecf09 · 8cecf09
2 parents 464b8c7 + bac129e
commit 8cecf09
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Showing 25 changed files with 75 additions and 62 deletions.
diff --git a/gtruby/core/alphabet.rb b/gtruby/core/alphabet.rb
@@ -74,7 +74,7 @@ def self.create_from_sequence(files)
       sa = StrArray.new
       files.each do |f|
         fn = f.to_s
-        if (!File.exists?(fn))
+        if (!File.exist?(fn))
           GT.gterror("file not found: #{fn}")
         end
         sa.add(fn)

diff --git a/gtruby/core/encseq.rb b/gtruby/core/encseq.rb
@@ -211,7 +211,7 @@ def encode(files, indexname)
       sa = StrArray.new
       files.each do |f|
         fn = f.to_s
-        if (!File.exists?(fn))
+        if (!File.exist?(fn))
           GT.gterror("file not found: #{fn}")
         end
         sa.add(fn)

diff --git a/scripts/add_revcmp.rb b/scripts/add_revcmp.rb
@@ -10,7 +10,7 @@ def initialize()
 	end
 
 	def read_sequence(file)
-		if !File.exists?(file)
+		if !File.exist?(file)
 			raise "The specified file #{file} does not exist."
 		end
 		File.open(file) do |line|
@@ -42,7 +42,7 @@ class MSA
   attr_reader :seqs, :length, :cons
 
   def initialize(file)
-    if !File.exists?(file)
+    if !File.exist?(file)
       raise "The specified file #{file} does not exist."
     end
     @file = file

diff --git a/scripts/appendsuffix.rb b/scripts/appendsuffix.rb
@@ -27,7 +27,7 @@
 
 end_usage
 
-if ARGV.size < 2 || !File.exists?(ARGV[0])
+if ARGV.size < 2 || !File.exist?(ARGV[0])
   puts usage
   exit
 end

diff --git a/scripts/cmp-seex-iter.rb b/scripts/cmp-seex-iter.rb
@@ -42,7 +42,7 @@
 end
 
 test_files.each do |filename|
-  if not File.exists?(filename)
+  if not File.exist?(filename)
     STDERR.puts "#{filename} does not exist"
     exit 1
   else

diff --git a/scripts/codegen b/scripts/codegen
@@ -113,7 +113,7 @@ end
 def prepare_tool_c(path, basename)
   tools_dir = File.join(find_src_directory, "tools")
   gt_template_c = File.expand_path(File.join(tools_dir, "gt_template.c"))
-  CodeGen.perror("File #{gt_template_c} not found") if !File.exists?(gt_template_c)
+  CodeGen.perror("File #{gt_template_c} not found") if !File.exist?(gt_template_c)
   # skip license template:
   c_template = IO.read(gt_template_c)
   c_template =~ /(.*?)(#include.*)/m
@@ -127,7 +127,7 @@ end
 def prepare_tool_h(path, basename)
   tools_dir = File.join(find_src_directory, "tools")
   gt_template_h = File.expand_path(File.join(tools_dir, "gt_template.h"))
-  CodeGen.perror("File #{gt_template_h} not found") if !File.exists?(gt_template_h)
+  CodeGen.perror("File #{gt_template_h} not found") if !File.exist?(gt_template_h)
   h_template = IO.read(gt_template_h)
   # skip license template:
   h_template =~ /(.*?)(#ifndef.*)/m

diff --git a/scripts/dwmake.rb b/scripts/dwmake.rb
@@ -141,7 +141,7 @@ def makecompilerflags(fp,options)
   fp.puts
 end
 
-if File.exists?('LocalMakefile')
+if File.exist?('LocalMakefile')
   FileUtils.mv('LocalMakefile','LocalMakefile.previous')
 end
 
@@ -151,7 +151,7 @@ def makecompilerflags(fp,options)
   makecompilerflags(fp,options)
 end
 
-if File.exists?('LocalMakefile.previous') and
+if File.exist?('LocalMakefile.previous') and
     not FileUtils.compare_file('LocalMakefile','LocalMakefile.previous') and
     options.check
   STDERR.puts "Current and previous LocalMakefile files differ: first " +

diff --git a/scripts/rdj-checkcontigs.rb b/scripts/rdj-checkcontigs.rb
@@ -34,7 +34,7 @@
 def get_template_index(templatefilename)
   indexname = "#{templatefilename}.vmatch"
   # the index is constructed only if necessary
-  unless File.exists?("#{indexname}.suf")
+  unless File.exist?("#{indexname}.suf")
     puts "# index #{indexname} not found, running mkvtree..."
     cmd = "mkvtree -dna -pl -allout -db #{templatefilename} "+
           "-indexname #{indexname}"

diff --git a/scripts/rdj-parsetranscript.rb b/scripts/rdj-parsetranscript.rb
@@ -2523,7 +2523,7 @@ def parse_series(args)
         next
       end
       if !logtype
-        if (!File.exists?(a))
+        if (!File.exist?(a))
           g = Dir.glob("#{a}*")
           if (g.size == 1)
             a = g[0]

diff --git a/scripts/sensitivity-test.rb b/scripts/sensitivity-test.rb
@@ -220,7 +220,7 @@ def callseedextend(mincoverage,indexname,inputfile,destfile,minidentity,length,
     matchlist = find_matchesinfile("#{destfile}.txt")
     ["esq","ssp"].each do |suffix|
       filename = "#{indexname}.#{suffix}"
-      if File.exists?(filename)
+      if File.exist?(filename)
         File.delete(filename)
       end
     end
@@ -231,7 +231,7 @@ def callseedextend(mincoverage,indexname,inputfile,destfile,minidentity,length,
 def runseedextend(mincoverage,inputdir,targetdir,weakends,withalignment,
                   seedlength,minidentity,length,seqnum,bias)
   inputfile = makefilename(inputdir,minidentity,"rand",length,seqnum)
-  if not File.exists?(inputfile + ".fas")
+  if not File.exist?(inputfile + ".fas")
     inputfile = makefilename(inputdir,minidentity,"rand-mult",length,seqnum)
   end
   destfile = makefilename(targetdir,minidentity,"gtout",length,seqnum)
@@ -244,7 +244,7 @@ def runseedextend(mincoverage,inputdir,targetdir,weakends,withalignment,
 def rundaligner(mincoverage,inputdir,targetdir,seedlength,minidentity,length,
                 seqnum,tofile = true)
   inputfile = makefilename(inputdir,minidentity,"rand",length,seqnum)
-  if not File.exists?(inputfile + ".fas")
+  if not File.exist?(inputfile + ".fas")
     inputfile = makefilename(inputdir,minidentity,"rand-mult",length,seqnum)
   end
   destfile = makefilename(targetdir,minidentity,"daout",length,seqnum)
@@ -294,7 +294,7 @@ def rerun_seedextend(options,seedlength)
   inputfiledir = options.inputdir
   puts # "minid=#{minidentity}, length=#{minidentity}, seqnum=#{seqnum}"
   inputfile = makefilename(inputfiledir,minidentity,"rand",length,seqnum)
-  if not File.exists?(inputfile + ".fas")
+  if not File.exist?(inputfile + ".fas")
     inputfile = makefilename(inputfiledir,minidentity,"rand-mult",length,seqnum)
   end
   puts "# inputfile=#{inputfile}.fas"

diff --git a/scripts/skmake.rb b/scripts/skmake.rb
@@ -109,7 +109,7 @@ def makecompilerflags(fp,options)
   end
 end
 
-if File.exists?('LocalMakefile')
+if File.exist?('LocalMakefile')
   FileUtils.mv('LocalMakefile','LocalMakefile.previous')
 end
 
@@ -119,7 +119,7 @@ def makecompilerflags(fp,options)
   makecompilerflags(fp,options)
 end
 
-if File.exists?('LocalMakefile.previous') and
+if File.exist?('LocalMakefile.previous') and
      not FileUtils.compare_file('LocalMakefile','LocalMakefile.previous')
   STDERR.puts "LocalMakefile and LocalMakefile.previous files differ: first " +
               "remove these"

diff --git a/scripts/sktest.sh b/scripts/sktest.sh
@@ -65,6 +65,6 @@ env -i GT_MEM_BOOKKEEPING=on ${program} -keywords 'gt_packedindex' \
 
 cd ..
 
-sktest-match.sh
+scripts/sktest-match.sh
 echo "start at ${startdate}"
 echo "end at `date`"
diff --git a/src/annotationsketch/custom_track_script_wrapper.h b/src/annotationsketch/custom_track_script_wrapper.h
@@ -22,6 +22,5 @@
 #include "annotationsketch/custom_track.h"
 
 const GtCustomTrackClass* gt_custom_track_script_wrapper_class(void);
-GtCustomTrack*            gt_custom_track_script_wrapper_new();
 
 #endif
diff --git a/src/core/csvline_reader.c b/src/core/csvline_reader.c
@@ -242,6 +242,7 @@ void gt_csvline_reader_dist_only_for_column(GtCsvlineReader *csvline_reader,
   csvline_reader->dist.alphabet.nextfreechar = write_idx;
 }
 
+#ifndef NDEBUG
 void gt_csvline_reader_dist_check(const GtCsvlineReader *csvline_reader,
                                   const char *string,GtUword len)
 {
@@ -259,15 +260,14 @@ void gt_csvline_reader_dist_check(const GtCsvlineReader *csvline_reader,
       numchars++;
     }
   }
-#ifndef NDEBUG
   gt_assert(numchars == csvline_reader->dist.alphabet.nextfreechar);
   for (idx = 0; idx < numchars; idx++)
   {
     char cc = csvline_reader->dist.alphabet.spacechar[idx];
     gt_assert(csvline_reader->dist.charcount[(int) cc] > 0);
   }
-#endif
 }
+#endif
 
 void gt_csvline_reader_dist_show(const GtCsvlineReader *csvline_reader)
 {

diff --git a/src/match/sfx-diffcov.c b/src/match/sfx-diffcov.c
@@ -1311,7 +1311,7 @@ static void dc_differencecover_sortsample(GtDifferencecover *dcov,
                                           GtTimer *sfxprogress,
                                           bool withcheck)
 {
-  GtUword pos, sampleindex, posinserted, fullspecials = 0, specials = 0;
+  GtUword pos, sampleindex, fullspecials = 0, specials = 0;
   unsigned int modvalue, unitsnotspecial;
   Diffvalue *diffptr, *afterend;
   GtCodetype code;
@@ -1419,8 +1419,12 @@ static void dc_differencecover_sortsample(GtDifferencecover *dcov,
   {
     gt_assert(dcov->sortedsample == NULL);
   }
-  posinserted = dc_derivespecialcodesonthefly(dcov,
-                                              withcheck ? &codelist : NULL);
+#ifndef NDEBUG
+  GtUword posinserted = 
+#else
+  (void)
+#endif
+  dc_derivespecialcodesonthefly(dcov,withcheck ? &codelist : NULL);
   GT_FREEARRAY(&codelist,Codeatposition);
   diffptr = dcov->diffvalues;
   afterend = dcov->diffvalues + dcov->size;
@@ -1444,7 +1448,9 @@ static void dc_differencecover_sortsample(GtDifferencecover *dcov,
                                                           code);
         gt_assert(sampleindex < dcov->effectivesamplesize);
         dc_suffixptrset(dcov,sampleindex,pos);
+#ifndef NDEBUG
         posinserted++;
+#endif
       }
       diffptr++;
     }

diff --git a/src/tools/gt_sfxmap.c b/src/tools/gt_sfxmap.c
@@ -909,10 +909,12 @@ static int gt_sfxmap_compressedesa(const char *indexname,GtError *err)
       unsigned int bits2add = (unsigned int) bitsperentry,
                    remainingbits = 0;
       GtUword bitbuffer = 0,
-                    countentries = 0,
                     *suftabptr,
                     *suftab = gt_malloc(sizeof *suftab *
                                         (size_t) numberofentries);
+#ifndef NDEBUG
+      GtUword countentries = 0;
+#endif
 
       suftabptr = suftab;
       while (true)
@@ -940,7 +942,9 @@ static int gt_sfxmap_compressedesa(const char *indexname,GtError *err)
             *suftabptr++ = bitbuffer;
             bitbuffer = 0;
             bits2add = (unsigned int) bitsperentry;
+#ifndef NDEBUG
             countentries++;
+#endif
           } else
           {
             gt_assert(remainingbits < 64U);
@@ -989,7 +993,9 @@ static int gt_sfxmap_compresslcp(const char *indexname,
   }
   if (!haserr)
   {
+#ifndef NDEBUG
     GtUword elems = 0;
+#endif
     GT_UNUSED GtUword totallength
       = gt_Sequentialsuffixarrayreader_totallength(ssar);
     GtUword maxbranchdepth
@@ -1018,7 +1024,9 @@ static int gt_sfxmap_compresslcp(const char *indexname,
 
           SSAR_NEXTSEQUENTIALLCPTABVALUE(currentlcp,ssar);
           gt_bitbuffer_write_fixed_bits_FILE (bitbuffer,currentlcp);
+#ifndef NDEBUG
           elems++;
+#endif
         }
       }
       if (!haserr)

diff --git a/testdata/gtruby/encseq.rb b/testdata/gtruby/encseq.rb
@@ -70,7 +70,7 @@ def delete_idx(indexname)
 
 val = create_es("foo")
 @idxsuffixes.each do |suf|
-  raise if !File.exists?("foo.#{suf}")
+  raise if !File.exist?("foo.#{suf}")
 end
 delete_idx("foo")
 

diff --git a/testsuite/gt_encseq2spm_include.rb b/testsuite/gt_encseq2spm_include.rb
@@ -39,7 +39,7 @@ def run_encseq2spm(readset)
   # compare results with precalculated known results
   [700, 7000].each do |nofreads|
     readset="#{$gttestdata}/readjoiner/#{nofreads}x_100nt_reads"
-    if File.exists?(readset)
+    if File.exist?(readset)
       Name "gt encseq2spm: #{nofreads}x100"
       Keywords "gt_encseq2spm"
       Test do
@@ -49,7 +49,7 @@ def run_encseq2spm(readset)
 
     [161, 200, 300, 400, 600, 1000].each do |len|
       reads = "#{$gttestdata}/readjoiner/#{nofreads}x_#{len}nt_reads"
-      if File.exists?(reads)
+      if File.exist?(reads)
         Name "gt encseq2spm: #{nofreads}x#{len}"
         Keywords "gt_encseq2spm"
         Test do

diff --git a/testsuite/gt_encseq_include.rb b/testsuite/gt_encseq_include.rb
@@ -246,7 +246,7 @@ def testformirrored(s, readmode)
     Keywords "gt_encseq formats"
     Test do
       fasta = formatfile.gsub(/\.[a-z]+$/, ".fna")
-      if File.exists?("#{$testdata}#{fasta}") then
+      if File.exist?("#{$testdata}#{fasta}") then
         run "cp #{$testdata}#{formatfile} infile"
         run_test "#{$bin}gt encseq encode -v -indexname sfx infile"
         run_test "#{$bin}gt encseq decode -output concat sfx > sfx.seq"

diff --git a/testsuite/gt_ltrdigest_include.rb b/testsuite/gt_ltrdigest_include.rb
@@ -430,7 +430,7 @@ def check_amino_acid_output(gff3file, chr, pdoms)
                "-hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm -- " + \
                "#{$gttestdata}ltrdigest/dmel_md5_4.gff3 ",
                :retval => 0, :maxtime => 12000
-      if File.exists?("result4_pdom_RVT_1.ali") then
+      if File.exist?("result4_pdom_RVT_1.ali") then
         raise TestFailed, "file \"result4_pdom_RVT_1.ali\" should not exist"
       end
       run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result4 " + \
@@ -439,7 +439,7 @@ def check_amino_acid_output(gff3file, chr, pdoms)
                "-aliout yes " + \
                "#{$gttestdata}ltrdigest/dmel_md5_4.gff3 ",
                :retval => 0, :maxtime => 12000
-      if !File.exists?("result4_pdom_RVT_1.ali") then
+      if !File.exist?("result4_pdom_RVT_1.ali") then
         raise TestFailed, "file \"result4_pdom_RVT_1.ali\" does not exist"
       end
     end
@@ -455,7 +455,7 @@ def check_amino_acid_output(gff3file, chr, pdoms)
                "-hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm -- " + \
                "#{$gttestdata}ltrdigest/dmel_md5_4.gff3 ",
                :retval => 0, :maxtime => 12000
-      if File.exists?("result4_pdom_RVT_1_aa.fas") then
+      if File.exist?("result4_pdom_RVT_1_aa.fas") then
         raise TestFailed, "file \"result4_pdom_RVT_1_aa.fas\" should not exist"
       end
       run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result4 " + \
@@ -464,7 +464,7 @@ def check_amino_acid_output(gff3file, chr, pdoms)
                "-aaout yes " + \
                "#{$gttestdata}ltrdigest/dmel_md5_4.gff3 ",
                :retval => 0, :maxtime => 12000
-      if !File.exists?("result4_pdom_RVT_1_aa.fas") then
+      if !File.exist?("result4_pdom_RVT_1_aa.fas") then
         raise TestFailed, "file \"result4_pdom_RVT_1_aa.fas\" does not exist"
       end
       if !(`grep ">" result4_pdom_RVT_1_aa.fas | wc -l`.to_i > 1) then
@@ -693,7 +693,7 @@ def check_amino_acid_output(gff3file, chr, pdoms)
                "#{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted " + \
                "4_genomic_dmel_RELEASE3-1.FASTA.gz", \
                :retval => 0, :maxtime => 12000
-      if File.exists?("result4_pdom_RVT_1.ali") then
+      if File.exist?("result4_pdom_RVT_1.ali") then
         raise TestFailed, "file \"result4_pdom_RVT_1.ali\" should not exist"
       end
       run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result4 " + \
@@ -702,7 +702,7 @@ def check_amino_acid_output(gff3file, chr, pdoms)
                "#{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted " + \
                "4_genomic_dmel_RELEASE3-1.FASTA.gz", \
                :retval => 0, :maxtime => 12000
-      if !File.exists?("result4_pdom_RVT_1.ali") then
+      if !File.exist?("result4_pdom_RVT_1.ali") then
         raise TestFailed, "file \"result4_pdom_RVT_1.ali\" does not exist"
       end
     end
@@ -718,7 +718,7 @@ def check_amino_acid_output(gff3file, chr, pdoms)
                "#{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted " + \
                "4_genomic_dmel_RELEASE3-1.FASTA.gz", \
                :retval => 0, :maxtime => 12000
-      if File.exists?("result4_pdom_RVT_1_aa.fas") then
+      if File.exist?("result4_pdom_RVT_1_aa.fas") then
         raise TestFailed, "file \"result4_pdom_RVT_1_aa.fas\" should not exist"
       end
       run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result4 " + \
@@ -727,7 +727,7 @@ def check_amino_acid_output(gff3file, chr, pdoms)
                "#{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted " + \
                "4_genomic_dmel_RELEASE3-1.FASTA.gz", \
                :retval => 0, :maxtime => 12000
-      if !File.exists?("result4_pdom_RVT_1_aa.fas") then
+      if !File.exist?("result4_pdom_RVT_1_aa.fas") then
         raise TestFailed, "file \"result4_pdom_RVT_1_aa.fas\" does not exist"
       end
     end