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R-bindings for interfacing with Tomahawk: computing and visualising linkage-disequilibrium data

Home Page: https://mklarqvist.github.io/tomahawk/

License: MIT License

R 66.99% C++ 33.01%
bioinformatics population-genetics visualization

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rtomahawk's Issues

Installation Issues

Hi,

I have been trying to install rtomahawk and have encountered this error:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/shabbeerhassan/R/x86_64-pc-linux-gnu-library/3.3/rtomahawk/libs/rtomahawk.so':
libhts.so.2to3part7: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed

  • removing ‘/home/shabbeerhassan/R/x86_64-pc-linux-gnu-library/3.3/rtomahawk’
    Error in i.p(...) :
    (converted from warning) installation of package ‘/tmp/Rtmphv1T9g/file7d27564aac4/rtomahawk_0.1.0.tar.gz’ had non-zero exit status

Is this because I don't have some file or rather path based issues?

Install make error

Hi,
I'm trying to get this installed on Ubuntu 20.04.6 LTS but am stuck here:

configure: error: cannot find required auxiliary files: config.guess config.sub
make: *** [Makevars:93: htslib] Error 1
ERROR: compilation failed for package ‘rtomahawk’

Any ideas?

Fails to build

Trying to build with devtools:

gcc -std=gnu99 -Wall -g -O2 -I.  -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -std=gnu99 -L/share/apps/centos7/java/1.8.0_171/lib  -o test/test-parse-reg test/test-parse-reg.o libhts.a -llzma -lbz2 -lz -lm   -lcurl -lcrypto -lpthread
make[1]: Leaving directory `/tmp/752440.1.all.q/Rtmpf7oI0t/R.INSTALL30fc66cd8577/rtomahawk/src/htslib'
cd tomahawk && make CC="gcc -std=gnu99" CXX="g++ " library library=true origin=true && cd ..
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
make[1]: Entering directory `/tmp/752440.1.all.q/Rtmpf7oI0t/R.INSTALL30fc66cd8577/rtomahawk/src/tomahawk'
g++  -std=c++0x -O3 -msse4.2 -fPIC  -I../htslib/ -I../zstd/lib/ -I../zstd/lib/common/ -I./include/ -I./lib/ -c -DVERSION=\"-\" -o lib/fisher_math.o lib/fisher_math.cpp
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
g++  -std=c++0x -O3 -msse4.2 -fPIC  -I../htslib/ -I../zstd/lib/ -I../zstd/lib/common/ -I./include/ -I./lib/ -c -DVERSION=\"-\" -o lib/intervals.o lib/intervals.cpp
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
g++  -std=c++0x -O3 -msse4.2 -fPIC  -I../htslib/ -I../zstd/lib/ -I../zstd/lib/common/ -I./include/ -I./lib/ -c -DVERSION=\"-\" -o lib/twk_reader.o lib/twk_reader.cpp
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
fatal: Not a git repository (or any parent up to mount point /tmp)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
g++  -std=c++0x -O3 -msse4.2 -fPIC  -I../htslib/ -I../zstd/lib/ -I../zstd/lib/common/ -I./include/ -I./lib/ -c -DVERSION=\"-\" -o lib/header_internal.o lib/header_internal.cpp
In file included from lib/header_internal.cpp:1:0:
lib/header_internal.h:16:44: error: expected class-name before ‘{’ token
 class VcfHeaderInternal : public VcfHeader {
                                            ^
lib/header_internal.h:37:23: error: ‘string’ in namespace ‘std’ does not name a type
  void AddSample(const std::string& sample_name);
                       ^
lib/header_internal.h:37:36: error: ISO C++ forbids declaration of ‘sample_name’ with no type [-fpermissive]
  void AddSample(const std::string& sample_name);
                                    ^
lib/header_internal.cpp: In function ‘const bcf_hrec_t* tomahawk::GetPopulatedHrec(const bcf_idpair_t&)’:
lib/header_internal.cpp:12:2: error: ‘cerr’ is not a member of ‘std’
  std::cerr << "No populated hrec in idPair. Error in htslib." << std::endl;
  ^
lib/header_internal.cpp:12:66: error: ‘endl’ is not a member of ‘std’
  std::cerr << "No populated hrec in idPair. Error in htslib." << std::endl;
                                                                  ^
lib/header_internal.cpp: In member function ‘void tomahawk::VcfHeaderInternal::AddContigInfo(const bcf_idpair_t&)’:
lib/header_internal.cpp:20:2: error: ‘VcfContig’ was not declared in this scope
  VcfContig c;
  ^
lib/header_internal.cpp:20:12: error: expected ‘;’ before ‘c’
  VcfContig c;
            ^
lib/header_internal.cpp:21:2: error: ‘c’ was not declared in this scope
  c.name = idPair.key;
  ^
lib/header_internal.cpp:27:9: error: ‘string’ in namespace ‘std’ does not name a type
   const std::string current_key(hrec0->keys[j]);
         ^
lib/header_internal.cpp:30:7: error: ‘current_key’ was not declared in this scope
   if (current_key == "ID" ||
       ^
lib/header_internal.cpp:37:22: error: ‘pair’ is not a member of ‘std’
    c.extra.push_back(std::pair<std::string,std::string>(current_key, std::string(hrec0->vals[j])));
                      ^
lib/header_internal.cpp:37:32: error: ‘string’ is not a member of ‘std’
    c.extra.push_back(std::pair<std::string,std::string>(current_key, std::string(hrec0->vals[j])));
                                ^
lib/header_internal.cpp:37:44: error: ‘string’ is not a member of ‘std’
    c.extra.push_back(std::pair<std::string,std::string>(current_key, std::string(hrec0->vals[j])));
                                            ^
lib/header_internal.cpp:37:70: error: ‘string’ is not a member of ‘std’
    c.extra.push_back(std::pair<std::string,std::string>(current_key, std::string(hrec0->vals[j])));
                                                                      ^
lib/header_internal.cpp:41:4: error: ‘cerr’ is not a member of ‘std’
    std::cerr << utility::timestamp("ERROR") << "hrec error" << std::endl;
    ^
lib/header_internal.cpp:41:17: error: ‘utility’ has not been declared
    std::cerr << utility::timestamp("ERROR") << "hrec error" << std::endl;
                 ^
lib/header_internal.cpp:41:64: error: ‘endl’ is not a member of ‘std’
    std::cerr << utility::timestamp("ERROR") << "hrec error" << std::endl;
                                                                ^
lib/header_internal.cpp:46:12: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘contigs_’
   if(this->contigs_.size() == 0){
            ^
lib/header_internal.cpp:47:10: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘contigs_’
    this->contigs_.push_back(c);
          ^
lib/header_internal.cpp:48:10: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘contigs_map_’
    this->contigs_map_[c.name] = 0;
          ^
lib/header_internal.cpp:52:12: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘contigs_map_’
   if(this->contigs_map_.find(c.name) == this->contigs_map_.end()){
            ^
lib/header_internal.cpp:52:47: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘contigs_map_’
   if(this->contigs_map_.find(c.name) == this->contigs_map_.end()){
                                               ^
lib/header_internal.cpp:53:10: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘contigs_map_’
    this->contigs_map_[c.name] = this->contigs_.size();
          ^
lib/header_internal.cpp:53:39: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘contigs_’
    this->contigs_map_[c.name] = this->contigs_.size();
                                       ^
lib/header_internal.cpp:54:10: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘contigs_’
    this->contigs_.push_back(c);
          ^
lib/header_internal.cpp:56:4: error: ‘cerr’ is not a member of ‘std’
    std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated contig name" << std::endl;
    ^
lib/header_internal.cpp:56:17: error: ‘utility’ has not been declared
    std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated contig name" << std::endl;
                 ^
lib/header_internal.cpp:56:85: error: ‘endl’ is not a member of ‘std’
    std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated contig name" << std::endl;
                                                                                     ^
lib/header_internal.cpp: In member function ‘void tomahawk::VcfHeaderInternal::AddFilterInfo(const bcf_hrec_t*)’:
lib/header_internal.cpp:63:27: error: ‘string’ is not a member of ‘std’
   if (hrec->nkeys >= 2 && std::string(hrec->keys[0]) == "ID" &&
                           ^
lib/header_internal.cpp:64:4: error: ‘string’ is not a member of ‘std’
    std::string(hrec->keys[1]) == "Description")
    ^
lib/header_internal.cpp:66:2: error: ‘VcfFilter’ was not declared in this scope
  VcfFilter f;
  ^
lib/header_internal.cpp:66:12: error: expected ‘;’ before ‘f’
  VcfFilter f;
            ^
lib/header_internal.cpp:67:2: error: ‘f’ was not declared in this scope
  f.id = std::string(hrec->vals[0]);
  ^
lib/header_internal.cpp:67:9: error: ‘string’ is not a member of ‘std’
  f.id = std::string(hrec->vals[0]);
         ^
lib/header_internal.cpp:68:18: error: ‘string’ is not a member of ‘std’
  f.description = std::string(hrec->vals[1]);
                  ^
lib/header_internal.cpp:70:6: error: ‘string’ is not a member of ‘std’
   if(std::string(hrec->keys[i]) == "IDX"){
      ^
lib/header_internal.cpp:76:11: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘filter_fields_’
  if(this->filter_fields_.size() == 0){
           ^
lib/header_internal.cpp:77:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘filter_fields_’
   this->filter_fields_.push_back(f);
         ^
lib/header_internal.cpp:78:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘filter_fields_map_’
   this->filter_fields_map_[f.id] = 0;
         ^
lib/header_internal.cpp:82:11: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘filter_fields_map_’
  if(this->filter_fields_map_.find(f.id) == this->filter_fields_map_.end()){
           ^
lib/header_internal.cpp:82:50: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘filter_fields_map_’
  if(this->filter_fields_map_.find(f.id) == this->filter_fields_map_.end()){
                                                  ^
lib/header_internal.cpp:83:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘filter_fields_map_’
   this->filter_fields_map_[f.id] = this->filter_fields_.size();
         ^
lib/header_internal.cpp:83:42: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘filter_fields_’
   this->filter_fields_map_[f.id] = this->filter_fields_.size();
                                          ^
lib/header_internal.cpp:84:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘filter_fields_’
   this->filter_fields_.push_back(f);
         ^
lib/header_internal.cpp:86:3: error: ‘cerr’ is not a member of ‘std’
   std::cerr << utility::timestamp("ERROR")  << "Illegal: duplicated filter name: " << f.id << std::endl;
   ^
lib/header_internal.cpp:86:16: error: ‘utility’ has not been declared
   std::cerr << utility::timestamp("ERROR")  << "Illegal: duplicated filter name: " << f.id << std::endl;
                ^
lib/header_internal.cpp:86:95: error: ‘endl’ is not a member of ‘std’
   std::cerr << utility::timestamp("ERROR")  << "Illegal: duplicated filter name: " << f.id << std::endl;
                                                                                               ^
lib/header_internal.cpp:91:2: error: ‘cerr’ is not a member of ‘std’
  std::cerr << utility::timestamp("ERROR") << "Malformed FILTER field detected in header, leaving this "
  ^
lib/header_internal.cpp:91:15: error: ‘utility’ has not been declared
  std::cerr << utility::timestamp("ERROR") << "Malformed FILTER field detected in header, leaving this "
               ^
lib/header_internal.cpp:92:24: error: ‘endl’ is not a member of ‘std’
      "filter empty" << std::endl;
                        ^
lib/header_internal.cpp: In member function ‘void tomahawk::VcfHeaderInternal::AddInfo(const bcf_hrec_t*)’:
lib/header_internal.cpp:98:27: error: ‘string’ is not a member of ‘std’
   if (hrec->nkeys >= 4 && std::string(hrec->keys[0]) == "ID" &&
                           ^
lib/header_internal.cpp:99:4: error: ‘string’ is not a member of ‘std’
    std::string(hrec->keys[1]) == "Number" && std::string(hrec->keys[2]) == "Type" &&
    ^
lib/header_internal.cpp:99:46: error: ‘string’ is not a member of ‘std’
    std::string(hrec->keys[1]) == "Number" && std::string(hrec->keys[2]) == "Type" &&
                                              ^
lib/header_internal.cpp:100:4: error: ‘string’ is not a member of ‘std’
    std::string(hrec->keys[3]) == "Description")
    ^
lib/header_internal.cpp:102:2: error: ‘VcfInfo’ was not declared in this scope
  VcfInfo f;
  ^
lib/header_internal.cpp:102:10: error: expected ‘;’ before ‘f’
  VcfInfo f;
          ^
lib/header_internal.cpp:103:2: error: ‘f’ was not declared in this scope
  f.id = std::string(hrec->vals[0]);
  ^
lib/header_internal.cpp:103:9: error: ‘string’ is not a member of ‘std’
  f.id = std::string(hrec->vals[0]);
         ^
lib/header_internal.cpp:104:13: error: ‘string’ is not a member of ‘std’
  f.number = std::string(hrec->vals[1]);
             ^
lib/header_internal.cpp:105:11: error: ‘string’ is not a member of ‘std’
  f.type = std::string(hrec->vals[2]);
           ^
lib/header_internal.cpp:106:18: error: ‘string’ is not a member of ‘std’
  f.description = std::string(hrec->vals[3]);
                  ^
lib/header_internal.cpp:108:10: error: ‘string’ in namespace ‘std’ does not name a type
    const std::string current_key = std::string(hrec->keys[i]);
          ^
lib/header_internal.cpp:109:8: error: ‘current_key’ was not declared in this scope
    if (current_key == "Source") {
        ^
lib/header_internal.cpp:110:14: error: ‘string’ is not a member of ‘std’
   f.source = std::string(hrec->vals[i]);
              ^
lib/header_internal.cpp:112:15: error: ‘string’ is not a member of ‘std’
   f.version = std::string(hrec->vals[i]);
               ^
lib/header_internal.cpp:119:11: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘info_fields_’
  if(this->info_fields_.size() == 0){
           ^
lib/header_internal.cpp:120:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘info_fields_’
   this->info_fields_.push_back(f);
         ^
lib/header_internal.cpp:121:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘info_fields_map_’
   this->info_fields_map_[f.id] = 0;
         ^
lib/header_internal.cpp:125:11: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘info_fields_map_’
  if(this->info_fields_map_.find(f.id) == this->info_fields_map_.end()){
           ^
lib/header_internal.cpp:125:48: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘info_fields_map_’
  if(this->info_fields_map_.find(f.id) == this->info_fields_map_.end()){
                                                ^
lib/header_internal.cpp:126:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘info_fields_map_’
   this->info_fields_map_[f.id] = this->info_fields_.size();
         ^
lib/header_internal.cpp:126:40: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘info_fields_’
   this->info_fields_map_[f.id] = this->info_fields_.size();
                                        ^
lib/header_internal.cpp:127:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘info_fields_’
   this->info_fields_.push_back(f);
         ^
lib/header_internal.cpp:129:3: error: ‘cerr’ is not a member of ‘std’
   std::cerr << utility::timestamp("ERROR")  << "Illegal: duplicated info name: " << f.id << std::endl;
   ^
lib/header_internal.cpp:129:16: error: ‘utility’ has not been declared
   std::cerr << utility::timestamp("ERROR")  << "Illegal: duplicated info name: " << f.id << std::endl;
                ^
lib/header_internal.cpp:129:93: error: ‘endl’ is not a member of ‘std’
   std::cerr << utility::timestamp("ERROR")  << "Illegal: duplicated info name: " << f.id << std::endl;
                                                                                             ^
lib/header_internal.cpp:134:2: error: ‘cerr’ is not a member of ‘std’
  std::cerr << utility::timestamp("ERROR") << "Malformed INFO field detected in header, leaving this "
  ^
lib/header_internal.cpp:134:15: error: ‘utility’ has not been declared
  std::cerr << utility::timestamp("ERROR") << "Malformed INFO field detected in header, leaving this "
               ^
lib/header_internal.cpp:135:22: error: ‘endl’ is not a member of ‘std’
      "info empty" << std::endl;
                      ^
lib/header_internal.cpp: In member function ‘void tomahawk::VcfHeaderInternal::AddFormatInfo(const bcf_hrec_t*)’:
lib/header_internal.cpp:141:27: error: ‘string’ is not a member of ‘std’
   if (hrec->nkeys >= 4 && std::string(hrec->keys[0]) == "ID" &&
                           ^
lib/header_internal.cpp:142:4: error: ‘string’ is not a member of ‘std’
    std::string(hrec->keys[1]) == "Number" && std::string(hrec->keys[2]) == "Type" &&
    ^
lib/header_internal.cpp:142:46: error: ‘string’ is not a member of ‘std’
    std::string(hrec->keys[1]) == "Number" && std::string(hrec->keys[2]) == "Type" &&
                                              ^
lib/header_internal.cpp:143:4: error: ‘string’ is not a member of ‘std’
    std::string(hrec->keys[3]) == "Description")
    ^
lib/header_internal.cpp:145:2: error: ‘VcfFormat’ was not declared in this scope
  VcfFormat f;
  ^
lib/header_internal.cpp:145:12: error: expected ‘;’ before ‘f’
  VcfFormat f;
            ^
lib/header_internal.cpp:146:2: error: ‘f’ was not declared in this scope
  f.id          = std::string(hrec->vals[0]);
  ^
lib/header_internal.cpp:146:18: error: ‘string’ is not a member of ‘std’
  f.id          = std::string(hrec->vals[0]);
                  ^
lib/header_internal.cpp:147:18: error: ‘string’ is not a member of ‘std’
  f.number      = std::string(hrec->vals[1]);
                  ^
lib/header_internal.cpp:148:18: error: ‘string’ is not a member of ‘std’
  f.type        = std::string(hrec->vals[2]);
                  ^
lib/header_internal.cpp:149:18: error: ‘string’ is not a member of ‘std’
  f.description = std::string(hrec->vals[3]);
                  ^
lib/header_internal.cpp:151:9: error: ‘string’ in namespace ‘std’ does not name a type
   const std::string current_key = std::string(hrec->keys[i]);
         ^
lib/header_internal.cpp:152:7: error: ‘current_key’ was not declared in this scope
   if (current_key == "IDX") {
       ^
lib/header_internal.cpp:158:11: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘format_fields_’
  if(this->format_fields_.size() == 0){
           ^
lib/header_internal.cpp:159:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘format_fields_’
   this->format_fields_.push_back(f);
         ^
lib/header_internal.cpp:160:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘format_fields_map_’
   this->format_fields_map_[f.id] = 0;
         ^
lib/header_internal.cpp:164:11: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘format_fields_map_’
  if(this->format_fields_map_.find(f.id) == this->format_fields_map_.end()){
           ^
lib/header_internal.cpp:164:50: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘format_fields_map_’
  if(this->format_fields_map_.find(f.id) == this->format_fields_map_.end()){
                                                  ^
lib/header_internal.cpp:165:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘format_fields_map_’
   this->format_fields_map_[f.id] = this->format_fields_.size();
         ^
lib/header_internal.cpp:165:42: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘format_fields_’
   this->format_fields_map_[f.id] = this->format_fields_.size();
                                          ^
lib/header_internal.cpp:166:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘format_fields_’
   this->format_fields_.push_back(f);
         ^
lib/header_internal.cpp:168:3: error: ‘cerr’ is not a member of ‘std’
   std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated format name: " << f.id << std::endl;
   ^
lib/header_internal.cpp:168:16: error: ‘utility’ has not been declared
   std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated format name: " << f.id << std::endl;
                ^
lib/header_internal.cpp:168:94: error: ‘endl’ is not a member of ‘std’
   std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated format name: " << f.id << std::endl;
                                                                                              ^
lib/header_internal.cpp:173:2: error: ‘cerr’ is not a member of ‘std’
  std::cerr << utility::timestamp("ERROR")  << "Malformed FORMAT field detected in header, leaving this "
  ^
lib/header_internal.cpp:173:15: error: ‘utility’ has not been declared
  std::cerr << utility::timestamp("ERROR")  << "Malformed FORMAT field detected in header, leaving this "
               ^
lib/header_internal.cpp:174:24: error: ‘endl’ is not a member of ‘std’
      "format empty" << std::endl;
                        ^
lib/header_internal.cpp: In member function ‘void tomahawk::VcfHeaderInternal::AddStructuredExtra(const bcf_hrec_t*)’:
lib/header_internal.cpp:180:3: error: ‘VcfStructuredExtra’ was not declared in this scope
   VcfStructuredExtra f;
   ^
lib/header_internal.cpp:180:22: error: expected ‘;’ before ‘f’
   VcfStructuredExtra f;
                      ^
lib/header_internal.cpp:181:3: error: ‘f’ was not declared in this scope
   f.key = std::string(hrec->key);
   ^
lib/header_internal.cpp:181:11: error: ‘string’ is not a member of ‘std’
   f.key = std::string(hrec->key);
           ^
lib/header_internal.cpp:183:32: error: ‘string’ is not a member of ‘std’
    f.fields.push_back(VcfExtra(std::string(hrec->keys[i]), std::string(hrec->vals[i])));
                                ^
lib/header_internal.cpp:183:60: error: ‘string’ is not a member of ‘std’
    f.fields.push_back(VcfExtra(std::string(hrec->keys[i]), std::string(hrec->vals[i])));
                                                            ^
lib/header_internal.cpp:183:86: error: ‘VcfExtra’ was not declared in this scope
    f.fields.push_back(VcfExtra(std::string(hrec->keys[i]), std::string(hrec->vals[i])));
                                                                                      ^
lib/header_internal.cpp:185:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘structured_extra_fields_’
   this->structured_extra_fields_.push_back(f);
         ^
lib/header_internal.cpp: In member function ‘void tomahawk::VcfHeaderInternal::AddExtra(const bcf_hrec_t*)’:
lib/header_internal.cpp:190:3: error: ‘VcfExtra’ was not declared in this scope
   VcfExtra f;
   ^
lib/header_internal.cpp:190:12: error: expected ‘;’ before ‘f’
   VcfExtra f;
            ^
lib/header_internal.cpp:191:3: error: ‘f’ was not declared in this scope
   f.key   = std::string(hrec->key);
   ^
lib/header_internal.cpp:191:13: error: ‘string’ is not a member of ‘std’
   f.key   = std::string(hrec->key);
             ^
lib/header_internal.cpp:192:13: error: ‘string’ is not a member of ‘std’
   f.value = std::string(hrec->value);
             ^
lib/header_internal.cpp:193:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘extra_fields_’
   this->extra_fields_.push_back(f);
         ^
lib/header_internal.cpp: At global scope:
lib/header_internal.cpp:196:41: error: ‘string’ in namespace ‘std’ does not name a type
 void VcfHeaderInternal::AddSample(const std::string& sample_name) {
                                         ^
lib/header_internal.cpp:196:54: error: ISO C++ forbids declaration of ‘sample_name’ with no type [-fpermissive]
 void VcfHeaderInternal::AddSample(const std::string& sample_name) {
                                                      ^
lib/header_internal.cpp: In member function ‘void tomahawk::VcfHeaderInternal::AddSample(const int&)’:
lib/header_internal.cpp:197:11: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘samples_’
  if(this->samples_.size() == 0){
           ^
lib/header_internal.cpp:198:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘samples_’
   this->samples_.push_back(sample_name);
         ^
lib/header_internal.cpp:199:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘samples_map_’
   this->samples_map_[sample_name] = 0;
         ^
lib/header_internal.cpp:203:11: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘samples_map_’
  if(this->samples_map_.find(sample_name) == this->samples_map_.end()){
           ^
lib/header_internal.cpp:203:51: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘samples_map_’
  if(this->samples_map_.find(sample_name) == this->samples_map_.end()){
                                                   ^
lib/header_internal.cpp:204:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘samples_map_’
   this->samples_map_[sample_name] = this->samples_.size();
         ^
lib/header_internal.cpp:204:43: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘samples_’
   this->samples_map_[sample_name] = this->samples_.size();
                                           ^
lib/header_internal.cpp:205:9: error: ‘class tomahawk::VcfHeaderInternal’ has no member named ‘samples_’
   this->samples_.push_back(sample_name);
         ^
lib/header_internal.cpp:207:3: error: ‘cerr’ is not a member of ‘std’
   std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated sample name: " << sample_name << std::endl;
   ^
lib/header_internal.cpp:207:16: error: ‘utility’ has not been declared
   std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated sample name: " << sample_name << std::endl;
                ^
lib/header_internal.cpp:207:101: error: ‘endl’ is not a member of ‘std’
   std::cerr << utility::timestamp("ERROR") << "Illegal: duplicated sample name: " << sample_name << std::endl;
                                                                                                     ^
make[1]: *** [lib/header_internal.o] Error 1
make[1]: Leaving directory `/tmp/752440.1.all.q/Rtmpf7oI0t/R.INSTALL30fc66cd8577/rtomahawk/src/tomahawk'
make: *** [twk] Error 2
ERROR: compilation failed for package ‘rtomahawk’
* removing ‘/data/home/aaw945/R/x86_64-pc-linux-gnu-library/3.5/rtomahawk’
Error: Failed to install 'rtomahawk' from GitHub:
  (converted from warning) installation of package ‘/tmp/752440.1.all.q/Rtmpj6aQIP/file7156698fc90b/rtomahawk_0.1.0.tar.gz’ had non-zero exit status
>

This is using R 3.5.3 Java 1.8.0 and GCC 4.8.5 on Centos 7.

plotAggregation error

I'm getting an error when I try to use the plotAggregation function. I seem to get the error if I choose a method in the aggregate function different than "count".

First, I created an aggregate file in CLI:
tomahawk aggregate -i chr13_all.fr02p0001.two -x 10000 -y 10000 -f r2 -r mean -c 0 -t 20 -O b -o chr13.r2.mean.c0.twa

This file is 24826 bytes (so not empty), but when I try to plot it like this:
library(rtomahawk) agg <- loadAggregate("chr13.r2.mean.c0.twa") plotAggregation(agg, normalize = TRUE)
I get the following error a warnings:

Error in col_breaks[j] = as.numeric(names(cumdist)[which.max(cumdist >= :
replacement has length zero
In addition: Warning messages:
1: In min(cumdist) : no non-missing arguments to min; returning Inf
2: In max(cumdist) : no non-missing arguments to max; returning -Inf
3: In min(cumdist) : no non-missing arguments to min; returning Inf

This is my sessionInfo:

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] rtomahawk_0.1.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 IRanges_2.4.8 XVector_0.10.0
[4] parallel_3.2.3 GenomicRanges_1.22.4 Rcpp_1.0.4.6
[7] S4Vectors_0.8.11 BiocGenerics_0.16.1 GenomeInfoDb_1.6.3
[10] stats4_3.2.3

Thank you,
Abraham

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