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License: GNU General Public License v3.0

R 51.09% C++ 48.85% C 0.05%

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pati-ni thjimmylee prete letaylor evanbiederstedt jacobhepkema sravanisaripalli6 shaokunan

scfind's Issues

findCell single gene

When searching cell type by single gene, get error:
Error in apply(cell_types_p, 1, prod) :
dim(X) must have a positive length In addition: Warning message:
In sapply(sapply(inds, function(x) { :
longer object length is not a multiple of shorter object length

Latest SingleCellExperiment breaks buildCellTypeIndex

An update to SingleCellExperiment causes buildCellTypeIndex to break producing the following error:
Error: $ operator not defined for this S4 class

I think it is this commit that changed ShallowSimpleListAssays to SimpleAssays:
Bioconductor/SummarizedExperiment@e8a159a

  library("scfind")
  library("SingleCellExperiment")
  data(tmfacs)
   sce.bladder <- readRDS(url(tmfacs[1]))
    sce.bladder_updated <- SingleCellExperiment(
        assays = list(counts = counts(sce.bladder)),
        colData = colData(sce.bladder)
    )
    scfind.index <- scfind::buildCellTypeIndex(
        sce = sce.bladder_updated,
        cell.type.label = "cell_type1",
        dataset.name = "Bladder",
        assay.name = "counts"
    )

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS/LAPACK: /home/ubuntu/miniconda3/envs/sc_analysis_nb/lib/libopenblasp-r0.3.7.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] SingleCellExperiment_1.8.0  SummarizedExperiment_1.16.1
 [3] DelayedArray_0.12.2         BiocParallel_1.20.1
 [5] matrixStats_0.56.0          Biobase_2.46.0
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0
 [9] IRanges_2.20.2              S4Vectors_0.24.3
[11] BiocGenerics_0.32.0         scfind_3.5.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4             later_1.0.0            compiler_3.6.2
 [4] pillar_1.4.3           XVector_0.26.0         bitops_1.0-6
 [7] tools_3.6.2            zlibbioc_1.32.0        digest_0.6.25
[10] lifecycle_0.2.0        tibble_2.1.3           gtable_0.3.0
[13] lattice_0.20-40        pkgconfig_2.0.3        rlang_0.4.5
[16] Matrix_1.2-18          shiny_1.4.0.2          fastmap_1.0.1
[19] GenomeInfoDbData_1.2.2 dplyr_0.8.5            htmlwidgets_1.5.1
[22] tidyselect_1.0.0       grid_3.6.2             DT_0.12
[25] glue_1.3.2             data.table_1.12.8      R6_2.4.1
[28] hash_2.2.6.1           purrr_0.3.3            ggplot2_3.3.0
[31] magrittr_1.5           codetools_0.2-16       promises_1.1.0
[34] scales_1.1.0           htmltools_0.4.0        assertthat_0.2.1
[37] xtable_1.8-4           mime_0.9               colorspace_1.4-1
[40] httpuv_1.5.2           RCurl_1.98-1.1         munsell_0.5.0
[43] crayon_1.3.4

Issue installing scfind

Hello,
I get these error messages when I try to install scfind. I need help in figuring out what is not working here. Thanks.

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

utils:::menuInstallLocal()
local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE)

if(nchar(pkg)) library(pkg, character.only=TRUE)})
Warning message:
package ‘remotes’ was built under R version 3.5.3

utils:::menuInstallLocal()
remotes::install_github("hemberg-lab/scfind")
Downloading GitHub repo hemberg-lab/scfind@master

checking for file 'C:\Users\hashime\AppData\Local\Temp\RtmpoJWtAD\remotes1eb03635222e\hemberg-lab-scfind-faafe41/DESCRIPTION' ...

√ checking for file 'C:\Users\hashime\AppData\Local\Temp\RtmpoJWtAD\remotes1eb03635222e\hemberg-lab-scfind-faafe41/DESCRIPTION' (406ms)

preparing 'scfind':

checking DESCRIPTION meta-information ...

checking DESCRIPTION meta-information ...

√ checking DESCRIPTION meta-information

cleaning src
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories
looking to see if a 'data/datalist' file should be added
building 'scfind_3.1.0.tar.gz'

installing source package 'scfind' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~~1/R/R-35~~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.5.0/library/Rcpp/include" -I"C:/Program Files/R/R-3.5.0/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
c:/Rtools/mingw_32/bin/g++ -I"C:/PROGRA~~1/R/R-35~~1.0/include" -DNDEBUG -I"C:/Program Files/R/R-3.5.0/library/Rcpp/include" -I"C:/Program Files/R/R-3.5.0/library/RcppArmadillo/include" -O2 -Wall -mtune=generic -c eliasFano.cpp -o eliasFano.o
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/cstdint:35:0,
from fp_growth.h:4,
from eliasFano.cpp:9:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
#error This file requires compiler and library support for the
^
In file included from eliasFano.cpp:9:0:
fp_growth.h:14:7: error: expected nested-name-specifier before 'Item'
using Item = std::string;
^
fp_growth.h:15:7: error: expected nested-name-specifier before 'Transaction'
using Transaction = std::vector;
^
fp_growth.h:16:7: error: expected nested-name-specifier before 'TransformedPrefixPath'
using TransformedPrefixPath = std::pair<Transaction, uint64_t>;
^
fp_growth.h:17:7: error: expected nested-name-specifier before 'Pattern'
using Pattern = std::pair<std::set, uint64_t>;
^
fp_growth.h:21:11: error: 'Item' does not name a type
const Item item;
^
fp_growth.h:22:5: error: 'uint64_t' does not name a type
uint64_t frequency;
^
fp_growth.h:23:10: error: 'shared_ptr' in namespace 'std' does not name a template type
std::shared_ptr node_link;
^
fp_growth.h:24:10: error: 'weak_ptr' in namespace 'std' does not name a template type
std::weak_ptr parent;
^
fp_growth.h:25:17: error: 'shared_ptr' is not a member of 'std'
std::vector<std::shared_ptr> children;
^
fp_growth.h:25:17: error: 'shared_ptr' is not a member of 'std'
fp_growth.h:25:42: error: 'children' was not declared in this scope
std::vector<std::shared_ptr> children;
^
fp_growth.h:25:42: error: template argument 1 is invalid
fp_growth.h:25:42: error: template argument 2 is invalid
fp_growth.h:27:18: error: 'Item' does not name a type
FPNode(const Item&, const std::shared_ptr&);
^
fp_growth.h:27:36: error: 'shared_ptr' in namespace 'std' does not name a template type
FPNode(const Item&, const std::shared_ptr&);
^
fp_growth.h:27:46: error: expected ',' or '...' before '<' token
FPNode(const Item&, const std::shared_ptr&);
^
fp_growth.h:31:10: error: 'shared_ptr' in namespace 'std' does not name a template type
std::shared_ptr root;
^
fp_growth.h:32:14: error: 'Item' was not declared in this scope
std::map<Item, std::shared_ptr> header_table;
^
fp_growth.h:32:20: error: 'shared_ptr' is not a member of 'std'
std::map<Item, std::shared_ptr> header_table;
^
fp_growth.h:32:20: error: 'shared_ptr' is not a member of 'std'
fp_growth.h:32:45: error: 'header_table' was not declared in this scope
std::map<Item, std::shared_ptr> header_table;
^
fp_growth.h:32:45: error: template argument 1 is invalid
fp_growth.h:32:45: error: template argument 2 is invalid
fp_growth.h:32:45: error: template argument 3 is invalid
fp_growth.h:32:45: error: template argument 4 is invalid
fp_growth.h:33:5: error: 'uint64_t' does not name a type
uint64_t minimum_support_threshold;
^
fp_growth.h:35:30: error: 'Transaction' was not declared in this scope
FPTree(const std::vector&, uint64_t);
^
fp_growth.h:35:41: error: template argument 1 is invalid
FPTree(const std::vector&, uint64_t);
^
fp_growth.h:35:41: error: template argument 2 is invalid
fp_growth.h:35:45: error: 'uint64_t' has not been declared
FPTree(const std::vector&, uint64_t);
^
fp_growth.h:41:10: error: 'Pattern' was not declared in this scope
std::set fptree_growth(const FPTree&);
^
fp_growth.h:41:17: error: template argument 1 is invalid
std::set fptree_growth(const FPTree&);
^
fp_growth.h:41:17: error: template argument 2 is invalid
fp_growth.h:41:17: error: template argument 3 is invalid
fp_growth.h:41:47: error: invalid type in declaration before ';' token
std::set fptree_growth(const FPTree&);
^
In file included from eliasFano.cpp:11:0:
EliasFano.h:88:10: error: 'hash' is not a class template
struct hash
^
EliasFano.h:89:3: error: explicit specialization of non-template 'std::hash'
{
^
EliasFano.h: In member function 'std::size_t std::hash::operator()(const CellID&) const':
EliasFano.h:92:14: error: 'std::hash' is not a template
return hash()(cid.cell_type) ^ hash()(cid.cell_id);
^
EliasFano.h:92:46: error: no match for call to '(std::hash) (const CellTypeID&)'
return hash()(cid.cell_type) ^ hash()(cid.cell_id);
^
EliasFano.h:88:10: note: candidate is:
struct hash
^
EliasFano.h:90:19: note: std::size_t std::hash::operator()(const CellID&) const
inline size_t operator()(const CellID& cid) const
^
EliasFano.h:90:19: note: no known conversion for argument 1 from 'const CellTypeID {aka const int}' to 'const CellID&'
EliasFano.h:92:50: error: 'std::hash' is not a template
return hash()(cid.cell_type) ^ hash()(cid.cell_id);
^
EliasFano.h:92:73: error: no match for call to '(std::hash) (const int&)'
return hash()(cid.cell_type) ^ hash()(cid.cell_id);
^
EliasFano.h:88:10: note: candidate is:
struct hash
^
EliasFano.h:90:19: note: std::size_t std::hash::operator()(const CellID&) const
inline size_t operator()(const CellID& cid) const
^
EliasFano.h:90:19: note: no known conversion for argument 1 from 'const int' to 'const CellID&'
EliasFano.h: At global scope:
EliasFano.h:114:8: error: 'unordered_map' in namespace 'std' does not name a template type
std::unordered_map<CellID , std::pair<std::vector, int> > tfidf;
^
In file included from eliasFano.cpp:11:0:
EliasFano.h:179:16: error: 'unordered_map' in namespace 'std' does not name a template type
typedef std::unordered_map<CellTypeID, EliasFanoID> GeneContainer;
^
EliasFano.h:180:30: error: 'GeneContainer' was not declared in this scope
typedef std::map<GeneName, GeneContainer> GeneExpressionDB;
^
EliasFano.h:180:43: error: template argument 2 is invalid
typedef std::map<GeneName, GeneContainer> GeneExpressionDB;
^
EliasFano.h:180:43: error: template argument 4 is invalid
EliasFano.h:184:16: error: 'unordered_map' in namespace 'std' does not name a template type
typedef std::unordered_map<CellID, CellMeta> CellIndex;
^
EliasFano.h:187:16: error: 'unordered_map' in namespace 'std' does not name a template type
typedef std::unordered_map<CellTypeName, CellTypeID> CellTypeIndex;
^
EliasFano.h:193:3: error: 'CellIndex' does not name a type
CellIndex cells;
^
EliasFano.h:194:3: error: 'CellTypeIndex' does not name a type
CellTypeIndex cell_types;
^
EliasFano.h:248:3: error: 'CellTypeIndex' does not name a type
CellTypeIndex getCellTypeIDs(const std::setstd::string& datasets) const;
^
eliasFano.cpp: In member function 'void QueryScore::cell_type_relevance(const EliasFanoDB&, const List&, const std::set<std::basic_string >&)':
eliasFano.cpp:75:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto it = ct_map.begin(); it != ct_map.end();)
^
eliasFano.cpp:75:13: error: 'it' does not name a type
for (auto it = ct_map.begin(); it != ct_map.end();)
^
eliasFano.cpp:75:34: error: expected ';' before 'it'
for (auto it = ct_map.begin(); it != ct_map.end();)
^
eliasFano.cpp:75:34: error: 'it' was not declared in this scope
eliasFano.cpp:80:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& _ct : ct_map)
^
eliasFano.cpp:80:26: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& _ct : ct_map)
^
eliasFano.cpp:83:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto cct = db.cell_types.find(_ct.first);
^
eliasFano.cpp:83:10: error: 'cct' does not name a type
auto cct = db.cell_types.find(_ct.first);
^
eliasFano.cpp:86:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& g : gene_set)
^
eliasFano.cpp:86:27: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& g : gene_set)
^
eliasFano.cpp:88:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto dbg = db.index.find(g);
^
eliasFano.cpp:88:12: error: 'dbg' does not name a type
auto dbg = db.index.find(g);
^
eliasFano.cpp:89:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto gct = dbg->second.find(cct->second);
^
eliasFano.cpp:89:12: error: 'gct' does not name a type
auto gct = dbg->second.find(cct->second);
^
eliasFano.cpp:90:13: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto& ef = db.ef_data[gct->second];
^
eliasFano.cpp:90:35: error: 'gct' was not declared in this scope
const auto& ef = db.ef_data[gct->second];
^
eliasFano.cpp:91:19: error: request for member 'idf' in 'ef', which is of non-class type 'const int'
tfidf += ef.idf;
^
eliasFano.cpp:86:23: warning: unused variable 'g' [-Wunused-variable]
for (auto const& g : gene_set)
^
eliasFano.cpp:93:36: error: request for member 'second' in '_ct', which is of non-class type 'const int'
query_score += tfidf * log(_ct.second.size());
^
eliasFano.cpp:94:27: error: request for member 'second' in '_ct', which is of non-class type 'const int'
cells_in_query += _ct.second.size();
^
eliasFano.cpp: In member function 'void QueryScore::estimateExpression(const List&, const EliasFanoDB&, const CharacterVector&, bool)':
eliasFano.cpp:113:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto& tmp_strings = Rcpp::as<std::vectorstd::string>(gene_results.names());
^
eliasFano.cpp:113:61: error: '>>' should be '> >' within a nested template argument list
const auto& tmp_strings = Rcpp::as<std::vectorstd::string>(gene_results.names());
^
eliasFano.cpp:113:84: error: invalid initialization of reference of type 'const int&' from expression of type 'std::vector<std::basic_string >'
const auto& tmp_strings = Rcpp::as<std::vectorstd::string>(gene_results.names());
^
eliasFano.cpp:114:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto tmpl_cont = std::vector(tmp_strings.size(), 0);
^
eliasFano.cpp:114:14: error: 'tmpl_cont' does not name a type
const auto tmpl_cont = std::vector(tmp_strings.size(), 0);
^
eliasFano.cpp:118:49: error: '>>' should be '> >' within a nested template argument list
std::vector gs = Rcpp::as<std::vector>(gene_support);
^
eliasFano.cpp:119:71: error: '>>' should be '> >' within a nested template argument list
std::vectorstd::string gs_names = Rcpp::as<std::vectorstd::string>(gene_support.names());
^
eliasFano.cpp:120:41: error: '>>' should be '> >' within a nested template argument list
std::vector<std::pair<std::string, int>> gs_pairs;
^
eliasFano.cpp:129:5: warning: lambda expressions only available with -std=c++11 or -std=gnu++11
});
^
eliasFano.cpp:129:6: error: no matching function for call to 'transform(std::vector::iterator, std::vector::iterator, std::vector<std::basic_string >::iterator, std::back_insert_iterator<std::vector<std::pair<std::basic_string, int> > >, QueryScore::estimateExpression(const List&, const EliasFanoDB&, const CharacterVector&, bool)::<lambda(const int&, const string&)>)'
});
^
eliasFano.cpp:129:6: note: candidates are:
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/algorithm:62:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:63,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_algo.h:4153:5: note: template<class _IIter, class _OIter, class _UnaryOperation> _OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation)
transform(_InputIterator __first, _InputIterator __last,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_algo.h:4153:5: note: template argument deduction/substitution failed:
eliasFano.cpp:129:6: note: candidate expects 4 arguments, 5 provided
});
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/algorithm:62:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:63,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_algo.h:4190:5: note: template<class _IIter1, class _IIter2, class _OIter, class _BinaryOperation> _OIter std::transform(_IIter1, _IIter1, _IIter2, _OIter, _BinaryOperation)
transform(_InputIterator1 __first1, _InputIterator1 __last1,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_algo.h:4190:5: note: template argument deduction/substitution failed:
eliasFano.cpp: In substitution of 'template<class _IIter1, class _IIter2, class _OIter, class _BinaryOperation> _OIter std::transform(_IIter1, _IIter1, _IIter2, _OIter, _BinaryOperation) [with _IIter1 = __gnu_cxx::__normal_iterator<int*, std::vector >; _IIter2 = __gnu_cxx::__normal_iterator<std::basic_string, std::vector<std::basic_string > >; _OIter = std::back_insert_iterator<std::vector<std::pair<std::basic_string, int> > >; _BinaryOperation = QueryScore::estimateExpression(const List&, const EliasFanoDB&, const CharacterVector&, bool)::<lambda(const int&, const string&)>]':
eliasFano.cpp:129:6: required from here
eliasFano.cpp:129:6: error: template argument for 'template<class _IIter1, class _IIter2, class _OIter, class _BinaryOperation> _OIter std::transform(_IIter1, _IIter1, _IIter2, _OIter, _BinaryOperation)' uses local type 'QueryScore::estimateExpression(const List&, const EliasFanoDB&, const CharacterVector&, bool)::<lambda(const int&, const string&)>'
});
^
eliasFano.cpp:129:6: error: trying to instantiate 'template<class _IIter1, class _IIter2, class _OIter, class _BinaryOperation> _OIter std::transform(_IIter1, _IIter1, _IIter2, _OIter, _BinaryOperation)'
eliasFano.cpp:140:38: error: request for member 'size' in 'tmp_strings', which is of non-class type 'const int'
bool estimate_cutoff = tmp_strings.size() > 7 ? true : false;
^
eliasFano.cpp:142:52: error: request for member 'size' in 'tmp_strings', which is of non-class type 'const int'
for (size_t gene_row = 0; gene_row < tmp_strings.size(); ++gene_row)
^
eliasFano.cpp:145:51: error: invalid types 'const int[size_t {aka unsigned int}]' for array subscript
const std::string& gene = tmp_strings[gene_row];
^
eliasFano.cpp:153:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto ct_names = Rcpp::as<std::vectorstd::string>(cts.names());
^
eliasFano.cpp:153:16: error: 'ct_names' does not name a type
const auto ct_names = Rcpp::as<std::vectorstd::string>(cts.names());
^
eliasFano.cpp:154:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for(auto const& cell_type : ct_names)
^
eliasFano.cpp:154:33: error: range-based 'for' loops are not allowed in C++98 mode
for(auto const& cell_type : ct_names)
^
eliasFano.cpp:154:33: error: 'ct_names' was not declared in this scope
eliasFano.cpp:157:13: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto ctid_it = db.cell_types.find(cell_type);
^
eliasFano.cpp:157:18: error: 'ctid_it' does not name a type
const auto ctid_it = db.cell_types.find(cell_type);
^
eliasFano.cpp:158:26: error: 'ctid_it' was not declared in this scope
CellTypeID ct_id = ctid_it->second;
^
eliasFano.cpp:159:85: error: invalid user-defined conversion from 'const int' to 'const CellTypeName& {aka const std::basic_string&}' [-fpermissive]
std::vector expr_values = decompressValues(db.getEntry(gene, cell_type).expr, db.quantization_bits);
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:53:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: candidate is: std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]
basic_string<_CharT, _Traits, _Alloc>::
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: no known conversion for argument 1 from 'const int' to 'const char*'
eliasFano.cpp:159:85: error: invalid conversion from 'int' to 'const char*' [-fpermissive]
std::vector expr_values = decompressValues(db.getEntry(gene, cell_type).expr, db.quantization_bits);
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:53:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: initializing argument 1 of 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]'
basic_string<_CharT, _Traits, _Alloc>::
^
eliasFano.cpp:165:12: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& cell_id : expr_indices)
^
eliasFano.cpp:165:34: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& cell_id : expr_indices)
^
eliasFano.cpp:170:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto ins_res = tfidf.insert(std::make_pair(cell, std::make_pair(tmpl_cont, 0)));
^
eliasFano.cpp:170:14: error: 'ins_res' does not name a type
auto ins_res = tfidf.insert(std::make_pair(cell, std::make_pair(tmpl_cont, 0)));
^
eliasFano.cpp:173:42: error: 'ins_res' was not declared in this scope
std::vector& tfidf_vec = ins_res.first->second.first;
^
eliasFano.cpp:176:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto& gene_support = ins_res.first->second.second;
^
eliasFano.cpp:180:63: error: 'const class EliasFanoDB' has no member named 'cells'
tfidf_vec[gene_row] = (expr_values[expr_index++] / db.cells.at(cell).reads) * gene_idf;
^
eliasFano.cpp:182:109: error: 'const class EliasFanoDB' has no member named 'cells'
console_message == true ? Rcpp::Rcout << "gene " << gene << " cell type " << cell_type << " " << db.cells.at(cell).reads << std::endl : Rcpp::Rcout << "";
^
eliasFano.cpp:194:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& c : this->tfidf)
^
eliasFano.cpp:194:26: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& c : this->tfidf)
^
eliasFano.cpp:194:32: error: 'class QueryScore' has no member named 'tfidf'
for (auto const& c : this->tfidf)
^
eliasFano.cpp:197:12: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& v : c.second.first)
^
eliasFano.cpp:197:28: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& v : c.second.first)
^
eliasFano.cpp:197:30: error: request for member 'second' in 'c', which is of non-class type 'const int'
for (auto const& v : c.second.first)
^
eliasFano.cpp:199:40: error: request for member 'second' in 'c', which is of non-class type 'const int'
genes_subset[i++] += v > 0 ? c.second.second - 1 : 0;
^
eliasFano.cpp:204:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto& v : this->genes)
^
eliasFano.cpp:204:20: error: range-based 'for' loops are not allowed in C++98 mode
for (auto& v : this->genes)
^
eliasFano.cpp:206:9: error: request for member 'second' in 'v', which is of non-class type 'int'
v.second.cartesian_product_sets = genes_subset[v.second.index];
^
eliasFano.cpp:206:56: error: request for member 'second' in 'v', which is of non-class type 'int'
v.second.cartesian_product_sets = genes_subset[v.second.index];
^
eliasFano.cpp:207:9: error: request for member 'second' in 'v', which is of non-class type 'int'
v.second.cartesian_product_sets /= this->genes.size();
^
eliasFano.cpp:208:13: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto& current_gene_name = v.first;
^
eliasFano.cpp:208:41: error: request for member 'first' in 'v', which is of non-class type 'int'
const auto& current_gene_name = v.first;
^
eliasFano.cpp: In lambda function:
eliasFano.cpp:214:28: error: no match for 'operator==' (operand types are 'const std::basic_string' and 'const int')
if(gs_pair.first == current_gene_name)
^
eliasFano.cpp:214:28: note: candidates are:
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:136:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/complex.h:68:13: note: bool operator==(const Rcomplex&, const Rcomplex&)
inline bool operator==( const Rcomplex& a, const Rcomplex& b) {
^
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/complex.h:68:13: note: no known conversion for argument 1 from 'const std::basic_string' to 'const Rcomplex&'
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/operators.h:29:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/sugar.h:30,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:74,
from functions.h:4,
from eliasFano.cpp:10:
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__Vector.h:118:1: note: template<int RTYPE, bool LHS_NA, class LHS_T, bool RHS_NA, class RHS_T> Rcpp::sugar::Comparator<RTYPE, Rcpp::sugar::equal, LHS_NA, LHS_T, RHS_NA, RHS_T> operator==(const Rcpp::VectorBase<RHS_RTYPE, RHS_NA, RHS_T>&, const Rcpp::VectorBase<RTYPE, RHS_NA, RHS_T>&)
operator==(
^
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__Vector.h:118:1: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const Rcpp::VectorBase<RHS_RTYPE, RHS_NA, RHS_T>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/operators.h:30:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/sugar.h:30,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:74,
from functions.h:4,
from eliasFano.cpp:10:
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:211:1: note: template<int RTYPE, bool NA, class T> Rcpp::sugar::Comparator_With_One_Value<RTYPE, Rcpp::sugar::equal, NA, T> operator==(const Rcpp::VectorBase<RHS_RTYPE, RHS_NA, RHS_T>&, typename Rcpp::traits::storage_type::type)
operator==(
^
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:211:1: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const Rcpp::VectorBase<RHS_RTYPE, RHS_NA, RHS_T>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/operators.h:30:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/sugar.h:30,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:74,
from functions.h:4,
from eliasFano.cpp:10:
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:231:1: note: template<int RTYPE, bool NA, class T> Rcpp::sugar::Comparator_With_One_Value<RTYPE, Rcpp::sugar::equal, NA, T> operator==(typename Rcpp::traits::storage_type::type, const Rcpp::VectorBase<RHS_RTYPE, RHS_NA, RHS_T>&)
operator==(
^
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/sugar/operators/logical_operators__Vector__primitive.h:231:1: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: mismatched types 'const Rcpp::VectorBase<RHS_RTYPE, RHS_NA, RHS_T>' and 'const int'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:64:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/complex:463:5: note: template bool std::operator==(const _Tp&, const std::complex<_Tp>&)
operator==(const _Tp& __x, const complex<_Tp>& __y)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/complex:463:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: mismatched types 'const std::complex<_Tp>' and 'const int'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:64:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/complex:458:5: note: template bool std::operator==(const std::complex<_Tp>&, const _Tp&)
operator==(const complex<_Tp>& __x, const _Tp& __y)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/complex:458:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::complex<_Tp>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:64:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/complex:453:5: note: template bool std::operator==(const std::complex<_Tp>&, const std::complex<_Tp>&)
operator==(const complex<_Tp>& __x, const complex<_Tp>& __y)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/complex:453:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::complex<_Tp>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/deque:64:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:60,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_deque.h:2029:5: note: template<class _Tp, class _Alloc> bool std::operator==(const std::deque<_Tp, _Alloc>&, const std::deque<_Tp, _Alloc>&)
operator==(const deque<_Tp, _Alloc>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_deque.h:2029:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::deque<_Tp, _Alloc>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/deque:64:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:60,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_deque.h:258:5: note: template<class _Tp, class _RefL, class _PtrL, class _RefR, class _PtrR> bool std::operator==(const std::_Deque_iterator<_Tp, _Ref, _Ptr>&, const std::_Deque_iterator<_Tp, _RefR, _PtrR>&)
operator==(const _Deque_iterator<_Tp, _RefL, _PtrL>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_deque.h:258:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::_Deque_iterator<_Tp, _Ref, _Ptr>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/deque:64:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:60,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_deque.h:251:5: note: template<class _Tp, class _Ref, class _Ptr> bool std::operator==(const std::_Deque_iterator<_Tp, _Ref, _Ptr>&, const std::_Deque_iterator<_Tp, _Ref, _Ptr>&)
operator==(const _Deque_iterator<_Tp, _Ref, _Ptr>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_deque.h:251:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::_Deque_iterator<_Tp, _Ref, _Ptr>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/list:63:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:55,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_list.h:1729:5: note: template<class _Tp, class _Alloc> bool std::operator==(const std::list<_Tp, _Alloc>&, const std::list<_Tp, _Alloc>&)
operator==(const list<_Tp, _Alloc>& __x, const list<_Tp, _Alloc>& __y)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_list.h:1729:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::list<_Tp, _Alloc>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/list:63:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:55,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_list.h:285:5: note: template bool std::operator==(const std::_List_iterator<_Tp>&, const std::_List_const_iterator<_Val>&)
operator==(const _List_iterator<_Val>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_list.h:285:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::_List_iterator<_Tp>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/vector:64:0,
from fp_growth.h:9,
from eliasFano.cpp:9:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_vector.h:1511:5: note: template<class _Tp, class _Alloc> bool std::operator==(const std::vector<_Tp, _Alloc>&, const std::vector<_Tp, _Alloc>&)
operator==(const vector<_Tp, _Alloc>& __x, const vector<_Tp, _Alloc>& __y)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_vector.h:1511:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::vector<_Tp, _Alloc>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/set:62:0,
from fp_growth.h:7,
from eliasFano.cpp:9:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_multiset.h:777:5: note: template<class _Key, class _Compare, class _Alloc> bool std::operator==(const std::multiset<_Key, _Compare, _Alloc>&, const std::multiset<_Key, _Compare, _Alloc>&)
operator==(const multiset<_Key, _Compare, _Alloc>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_multiset.h:777:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::multiset<_Key, _Compare, _Alloc>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/set:61:0,
from fp_growth.h:7,
from eliasFano.cpp:9:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_set.h:793:5: note: template<class _Key, class _Compare, class _Alloc> bool std::operator==(const std::set<_Key, _Compare, _Alloc>&, const std::set<_Key, _Compare, _Alloc>&)
operator==(const set<_Key, _Compare, _Alloc>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_set.h:793:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::set<_Key, _Compare, _Alloc>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/map:62:0,
from fp_growth.h:5,
from eliasFano.cpp:9:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_multimap.h:903:5: note: template<class _Key, class _Tp, class _Compare, class _Alloc> bool std::operator==(const std::multimap<_Key, _Tp, _Compare, _Alloc>&, const std::multimap<_Key, _Tp, _Compare, _Alloc>&)
operator==(const multimap<_Key, _Tp, _Compare, _Alloc>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_multimap.h:903:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::multimap<_Key, _Tp, _Compare, _Alloc>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/map:61:0,
from fp_growth.h:5,
from eliasFano.cpp:9:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_map.h:1000:5: note: template<class _Key, class _Tp, class _Compare, class _Alloc> bool std::operator==(const std::map<_Key, _Tp, _Compare, _Alloc>&, const std::map<_Key, _Tp, _Compare, _Alloc>&)
operator==(const map<_Key, _Tp, _Compare, _Alloc>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_map.h:1000:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::map<_Key, _Tp, _Compare, _Alloc>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/map:60:0,
from fp_growth.h:5,
from eliasFano.cpp:9:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_tree.h:970:5: note: template<class _Key, class _Val, class _KeyOfValue, class _Compare, class _Alloc> bool std::operator==(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&)
operator==(const _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_tree.h:970:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/map:60:0,
from fp_growth.h:5,
from eliasFano.cpp:9:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_tree.h:323:5: note: template bool std::operator==(const std::_Rb_tree_iterator<_Tp>&, const std::_Rb_tree_const_iterator<_Val>&)
operator==(const _Rb_tree_iterator<_Val>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_tree.h:323:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::_Rb_tree_iterator<_Tp>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:66:0,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stream_iterator.h:130:5: note: template<class _Tp, class _CharT, class _Traits, class _Dist> bool std::operator==(const std::istream_iterator<_Tp, _CharT, _Traits, _Dist>&, const std::istream_iterator<_Tp, _CharT, _Traits, _Dist>&)
operator==(const istream_iterator<_Tp, _CharT, _Traits, _Dist>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stream_iterator.h:130:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::istream_iterator<_Tp, _CharT, _Traits, _Dist>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_facets.h:48:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_ios.h:37,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:44,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/streambuf_iterator.h:204:5: note: template<class _CharT, class _Traits> bool std::operator==(const std::istreambuf_iterator<_CharT, _Traits>&, const std::istreambuf_iterator<_CharT, _Traits>&)
operator==(const istreambuf_iterator<_CharT, _Traits>& __a,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/streambuf_iterator.h:204:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::istreambuf_iterator<_CharT, _Traits>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:52:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.h:2538:5: note: template<class _CharT, class _Traits, class _Alloc> bool std::operator==(const std::basic_string<_CharT, _Traits, _Alloc>&, const _CharT*)
operator==(const basic_string<_CharT, _Traits, _Alloc>& __lhs,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.h:2538:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: mismatched types 'const _CharT*' and 'int'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:52:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.h:2526:5: note: template<class _CharT, class _Traits, class _Alloc> bool std::operator==(const _CharT*, const std::basic_string<_CharT, _Traits, _Alloc>&)
operator==(const _CharT* __lhs,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.h:2526:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: mismatched types 'const _CharT*' and 'std::basic_string'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:52:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.h:2512:5: note: template typename __gnu_cxx::__enable_if<std::__is_char<_Tp>::__value, bool>::__type std::operator==(const std::basic_string<_CharT>&, const std::basic_string<_CharT>&)
operator==(const basic_string<_CharT>& __lhs,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.h:2512:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: mismatched types 'const std::basic_string<_CharT>' and 'const int'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:52:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.h:2505:5: note: template<class _CharT, class _Traits, class _Alloc> bool std::operator==(const std::basic_string<_CharT, _Traits, _Alloc>&, const std::basic_string<_CharT, _Traits, _Alloc>&)
operator==(const basic_string<_CharT, _Traits, _Alloc>& __lhs,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.h:2505:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: mismatched types 'const std::basic_string<_CharT, _Traits, _Alloc>' and 'const int'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:41:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/allocator.h:133:5: note: template bool std::operator==(const std::allocator<_CharT>&, const std::allocator<_CharT>&)
operator==(const allocator<_Tp>&, const allocator<_Tp>&)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/allocator.h:133:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::allocator<_CharT>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:41:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/allocator.h:128:5: note: template<class _T1, class _T2> bool std::operator==(const std::allocator<_CharT>&, const std::allocator<_T2>&)
operator==(const allocator<_T1>&, const allocator<_T2>&)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/allocator.h:128:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::allocator<_CharT>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_algobase.h:64:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/char_traits.h:39,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_pair.h:214:5: note: template<class _T1, class _T2> bool std::operator==(const std::pair<_T1, _T2>&, const std::pair<_T1, _T2>&)
operator==(const pair<_T1, _T2>& __x, const pair<_T1, _T2>& __y)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_pair.h:214:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::pair<_T1, _T2>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iosfwd:40:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/postypes.h:216:5: note: template bool std::operator==(const std::fpos<_StateT>&, const std::fpos<_StateT>&)
operator==(const fpos<_StateT>& __lhs, const fpos<_StateT>& __rhs)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/postypes.h:216:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::fpos<_StateT>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:63:0,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_iterator.h:342:5: note: template<class _IteratorL, class _IteratorR> bool std::operator==(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_IteratorR>&)
operator==(const reverse_iterator<_IteratorL>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_iterator.h:342:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::reverse_iterator<_Iterator>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:63:0,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_iterator.h:292:5: note: template bool std::operator==(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_Iterator>&)
operator==(const reverse_iterator<_Iterator>& __x,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_iterator.h:292:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const std::reverse_iterator<_Iterator>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/i686-w64-mingw32/bits/c++allocator.h:33:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/allocator.h:46,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ext/new_allocator.h:139:5: note: template bool __gnu_cxx::operator==(const __gnu_cxx::new_allocator<_Tp>&, const __gnu_cxx::new_allocator<_Tp>&)
operator==(const new_allocator<_Tp>&, const new_allocator<_Tp>&)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ext/new_allocator.h:139:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const __gnu_cxx::new_allocator<_Tp>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:63:0,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_iterator.h:815:5: note: template<class _Iterator, class _Container> bool __gnu_cxx::operator==(const __gnu_cxx::__normal_iterator<_Iterator, _Container>&, const __gnu_cxx::__normal_iterator<_Iterator, _Container>&)
operator==(const __normal_iterator<_Iterator, _Container>& __lhs,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_iterator.h:815:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const __gnu_cxx::__normal_iterator<_Iterator, _Container>'
if(gs_pair.first == current_gene_name)
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:63:0,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_iterator.h:808:5: note: template<class _IteratorL, class _IteratorR, class _Container> bool __gnu_cxx::operator==(const __gnu_cxx::__normal_iterator<_IteratorL, _Container>&, const __gnu_cxx::__normal_iterator<_IteratorR, _Container>&)
operator==(const __normal_iterator<_IteratorL, _Container>& __lhs,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_iterator.h:808:5: note: template argument deduction/substitution failed:
eliasFano.cpp:214:31: note: 'const std::basic_string' is not derived from 'const __gnu_cxx::__normal_iterator<_IteratorL, _Container>'
if(gs_pair.first == current_gene_name)
^
eliasFano.cpp: In member function 'void QueryScore::estimateExpression(const List&, const EliasFanoDB&, const CharacterVector&, bool)':
eliasFano.cpp:219:9: warning: lambda expressions only available with -std=c++11 or -std=gnu++11
});
^
eliasFano.cpp:219:10: error: no matching function for call to 'accumulate(std::vector<std::pair<std::basic_string, int> >::iterator, std::vector<std::pair<std::basic_string, int> >::iterator, int, QueryScore::estimateExpression(const List&, const EliasFanoDB&, const CharacterVector&, bool)::<lambda(const int&, const std::pair<std::basic_string, int>&)>)'
});
^
eliasFano.cpp:219:10: note: candidates are:
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/numeric:62:0,
from eliasFano.cpp:3:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_numeric.h:120:5: note: template<class _InputIterator, class _Tp> _Tp std::accumulate(_InputIterator, _InputIterator, _Tp)
accumulate(_InputIterator __first, _InputIterator __last, _Tp __init)
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_numeric.h:120:5: note: template argument deduction/substitution failed:
eliasFano.cpp:219:10: note: candidate expects 3 arguments, 4 provided
});
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/numeric:62:0,
from eliasFano.cpp:3:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_numeric.h:146:5: note: template<class _InputIterator, class _Tp, class _BinaryOperation> _Tp std::accumulate(_InputIterator, _InputIterator, _Tp, _BinaryOperation)
accumulate(_InputIterator __first, _InputIterator __last, _Tp __init,
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/stl_numeric.h:146:5: note: template argument deduction/substitution failed:
eliasFano.cpp: In substitution of 'template<class _InputIterator, class _Tp, class _BinaryOperation> _Tp std::accumulate(_InputIterator, _InputIterator, _Tp, _BinaryOperation) [with _InputIterator = __gnu_cxx::__normal_iterator<std::pair<std::basic_string, int>, std::vector<std::pair<std::basic_string, int> > >; _Tp = int; _BinaryOperation = QueryScore::estimateExpression(const List&, const EliasFanoDB&, const CharacterVector&, bool)::<lambda(const int&, const std::pair<std::basic_string, int>&)>]':
eliasFano.cpp:219:10: required from here
eliasFano.cpp:219:10: error: template argument for 'template<class _InputIterator, class _Tp, class _BinaryOperation> _Tp std::accumulate(_InputIterator, _InputIterator, _Tp, _BinaryOperation)' uses local type 'QueryScore::estimateExpression(const List&, const EliasFanoDB&, const CharacterVector&, bool)::<lambda(const int&, const std::pair<std::basic_string, int>&)>'
});
^
eliasFano.cpp:219:10: error: trying to instantiate 'template<class _InputIterator, class _Tp, class _BinaryOperation> _Tp std::accumulate(_InputIterator, _InputIterator, _Tp, _BinaryOperation)'
eliasFano.cpp:220:47: error: 'tfidf' was not declared in this scope
float mean_overlap = float(union_sum) / tfidf.size(); // normalize by cell size
^
eliasFano.cpp:223:9: error: request for member 'second' in 'v', which is of non-class type 'int'
v.second.cartesian_product_sets = mean_overlap;
^
eliasFano.cpp:226:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& v : this->genes)
^
eliasFano.cpp:226:26: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& v : this->genes)
^
eliasFano.cpp:228:55: error: request for member 'first' in 'v', which is of non-class type 'const int'
Rcpp::Rcerr << "Cutoff proposed for gene " << v.first << ": " << v.second.cartesian_product_sets <<" with support " << gs_pairs[i++].second << std::endl;
^
eliasFano.cpp:228:74: error: request for member 'second' in 'v', which is of non-class type 'const int'
Rcpp::Rcerr << "Cutoff proposed for gene " << v.first << ": " << v.second.cartesian_product_sets <<" with support " << gs_pairs[i++].second << std::endl;
^
eliasFano.cpp:233:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto& v : this->genes)
^
eliasFano.cpp:233:20: error: range-based 'for' loops are not allowed in C++98 mode
for (auto& v : this->genes)
^
eliasFano.cpp:235:9: error: request for member 'second' in 'v', which is of non-class type 'int'
v.second.cartesian_product_sets = 1;
^
eliasFano.cpp: In member function 'void QueryScore::cell_tfidf(const EliasFanoDB&, const std::set<std::basic_string >&)':
eliasFano.cpp:248:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for(auto const& g : gene_set)
^
eliasFano.cpp:248:23: error: range-based 'for' loops are not allowed in C++98 mode
for(auto const& g : gene_set)
^
eliasFano.cpp:250:26: error: invalid user-defined conversion from 'const int' to 'const key_type& {aka const std::basic_string&}' [-fpermissive]
float tfidf = genes[g].tfidf;
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:53:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: candidate is: std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]
basic_string<_CharT, _Traits, _Alloc>::
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: no known conversion for argument 1 from 'const int' to 'const char'
eliasFano.cpp:250:26: error: invalid conversion from 'int' to 'const char*' [-fpermissive]
float tfidf = genes[g].tfidf;
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:53:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: initializing argument 1 of 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]'
basic_string<_CharT, _Traits, _Alloc>::
^
eliasFano.cpp: In member function 'void EliasFanoDB::clearDB()':
eliasFano.cpp:271:9: error: request for member 'clear' in '((EliasFanoDB*)this)->EliasFanoDB::index', which is of non-class type 'EliasFanoDB::GeneExpressionDB {aka int}'
index.clear();
^
eliasFano.cpp:272:3: error: 'cell_types' was not declared in this scope
cell_types.clear();
^
eliasFano.cpp: In member function 'long int EliasFanoDB::eliasFanoCoding(const std::vector&, const NumericVector&)':
eliasFano.cpp:314:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto expr = ids.begin(); expr != ids.end(); ++expr)
^
eliasFano.cpp:314:13: error: 'expr' does not name a type
for (auto expr = ids.begin(); expr != ids.end(); ++expr)
^
eliasFano.cpp:314:33: error: expected ';' before 'expr'
for (auto expr = ids.begin(); expr != ids.end(); ++expr)
^
eliasFano.cpp:314:33: error: 'expr' was not declared in this scope
eliasFano.cpp: In member function 'std::vector EliasFanoDB::eliasFanoDecoding(const EliasFano&) const':
eliasFano.cpp:351:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto prev_it = H.begin() - 1;
^
eliasFano.cpp:351:8: error: 'prev_it' does not name a type
auto prev_it = H.begin() - 1;
^
eliasFano.cpp:353:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto true_it = std::find(H.begin(), H.end(), true);
^
eliasFano.cpp:353:13: error: 'true_it' does not name a type
for (auto true_it = std::find(H.begin(), H.end(), true);
^
eliasFano.cpp:354:8: error: expected ';' before 'true_it'
true_it != H.end() && i < ids.size();
^
eliasFano.cpp:354:8: error: 'true_it' was not declared in this scope
eliasFano.cpp:357:36: error: 'prev_it' was not declared in this scope
size_t offset = std::distance(prev_it, true_it);
^
eliasFano.cpp: In member function 'const CellType& EliasFanoDB::getCellType(const CellTypeName&) const':
eliasFano.cpp:375:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto id = this->cell_types.at(name);
^
eliasFano.cpp:375:8: error: 'id' does not name a type
auto id = this->cell_types.at(name);
^
eliasFano.cpp:376:38: error: 'id' was not declared in this scope
return this->inverse_cell_type.at(id);
^
eliasFano.cpp: In member function 'const NumericMatrix EliasFanoDB::getCellTypeMatrix(const CellTypeName&) const':
eliasFano.cpp:384:34: error: 'const class EliasFanoDB' has no member named 'cell_types'
const CellTypeID ct_id = this->cell_types.at(cell_type);
^
eliasFano.cpp:388:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& record : index)
^
eliasFano.cpp:388:29: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& record : index)
^
eliasFano.cpp:390:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto rec_it = record.second.find(ct_id);
^
eliasFano.cpp:390:10: error: 'rec_it' does not name a type
auto rec_it = record.second.find(ct_id);
^
eliasFano.cpp:391:9: error: 'rec_it' was not declared in this scope
if (rec_it != record.second.end())
^
eliasFano.cpp:391:26: error: request for member 'second' in 'record', which is of non-class type 'const int'
if (rec_it != record.second.end())
^
eliasFano.cpp:393:38: error: request for member 'first' in 'record', which is of non-class type 'const int'
feature_names.push_back(record.first);
^
eliasFano.cpp:406:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto& rec = getEntry(feature_names[row], cell_type);
^
eliasFano.cpp:406:61: error: invalid initialization of reference of type 'const int&' from expression of type 'const EliasFano'
const auto& rec = getEntry(feature_names[row], cell_type);
^
eliasFano.cpp:407:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto indices_val = eliasFanoDecoding(rec);
^
eliasFano.cpp:407:16: error: 'indices_val' does not name a type
const auto indices_val = eliasFanoDecoding(rec);
^
eliasFano.cpp:408:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto exp_val = decompressValues(rec.expr, qb);
^
eliasFano.cpp:408:16: error: 'exp_val' does not name a type
const auto exp_val = decompressValues(rec.expr, qb);
^
eliasFano.cpp:410:9: error: 'indices_val' was not declared in this scope
if (indices_val.size() != exp_val.size())
^
eliasFano.cpp:410:31: error: 'exp_val' was not declared in this scope
if (indices_val.size() != exp_val.size())
^
eliasFano.cpp:416:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto exp_it = exp_val.begin();
^
eliasFano.cpp:416:10: error: 'exp_it' does not name a type
auto exp_it = exp_val.begin();
^
eliasFano.cpp:418:9: error: 'exp_val' was not declared in this scope
if (exp_val.size() != indices_val.size())
^
eliasFano.cpp:418:27: error: 'indices_val' was not declared in this scope
if (exp_val.size() != indices_val.size())
^
eliasFano.cpp:425:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& index : indices_val)
^
eliasFano.cpp:425:30: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& index : indices_val)
^
eliasFano.cpp:425:30: error: 'indices_val' was not declared in this scope
eliasFano.cpp:427:29: error: 'exp_it' was not declared in this scope
na_vec[index - 1] = (exp_it);
^
eliasFano.cpp:406:17: warning: unused variable 'rec' [-Wunused-variable]
const auto& rec = getEntry(feature_names[row], cell_type);
^
eliasFano.cpp:384:20: warning: unused variable 'ct_id' [-Wunused-variable]
const CellTypeID ct_id = this->cell_types.at(cell_type);
^
eliasFano.cpp:401:7: warning: unused variable 'qb' [-Wunused-variable]
int qb = quantization_bits;
^
eliasFano.cpp: In member function 'const EliasFano& EliasFanoDB::getEntry(const GeneName&, const CellTypeName&) const':
eliasFano.cpp:448:41: error: request for member 'at' in '((const EliasFanoDB)this)->EliasFanoDB::index', which is of non-class type 'const GeneExpressionDB {aka const int}'
return this->ef_data.at(this->index.at(gene_name).at(this->cell_types.at(cell_type)));
^
eliasFano.cpp:448:64: error: 'const class EliasFanoDB' has no member named 'cell_types'
return this->ef_data.at(this->index.at(gene_name).at(this->cell_types.at(cell_type)));
^
eliasFano.cpp:453:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto g_it = index.find(gene_name);
^
eliasFano.cpp:453:10: error: 'g_it' does not name a type
auto g_it = index.find(gene_name);
^
eliasFano.cpp:454:9: error: 'g_it' was not declared in this scope
if (g_it == index.end())
^
eliasFano.cpp:454:23: error: request for member 'end' in '((const EliasFanoDB*)this)->EliasFanoDB::index', which is of non-class type 'const GeneExpressionDB {aka const int}'
if (g_it == index.end())
^
eliasFano.cpp:458:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto ct_it = this->cell_types.find(cell_type);
^
eliasFano.cpp:458:10: error: 'ct_it' does not name a type
auto ct_it = this->cell_types.find(cell_type);
^
eliasFano.cpp:460:9: error: 'ct_it' was not declared in this scope
if (ct_it == this->cell_types.end())
^
eliasFano.cpp:460:24: error: 'const class EliasFanoDB' has no member named 'cell_types'
if (ct_it == this->cell_types.end())
^
eliasFano.cpp:466:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto ef_it = g_it->second.find(ct_it->second);
^
eliasFano.cpp:466:12: error: 'ef_it' does not name a type
auto ef_it = g_it->second.find(ct_it->second);
^
eliasFano.cpp:468:10: error: 'ef_it' was not declared in this scope
if(ef_it == g_it->second.end())
^
eliasFano.cpp:468:19: error: 'g_it' was not declared in this scope
if(ef_it == g_it->second.end())
^
eliasFano.cpp: In member function 'int EliasFanoDB::queryZeroGeneSupport(const CharacterVector&) const':
eliasFano.cpp:493:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for(auto const& g : this->index)
^
eliasFano.cpp:493:23: error: range-based 'for' loops are not allowed in C++98 mode
for(auto const& g : this->index)
^
eliasFano.cpp:495:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto cell_support = this->totalCells(Rcpp::wrap(g.first), datasets);
^
eliasFano.cpp:495:10: error: 'cell_support' does not name a type
auto cell_support = this->totalCells(Rcpp::wrap(g.first), datasets);
^
eliasFano.cpp:497:9: error: 'cell_support' was not declared in this scope
if (cell_support[0] == 0){
^
eliasFano.cpp:499:35: error: request for member 'first' in 'g', which is of non-class type 'const int'
Rcpp::Rcerr << "Gene " << g.first << " found no support with " << g.second.size() << " cell types"<< std::endl;
^
eliasFano.cpp:499:76: error: request for member 'second' in 'g', which is of non-class type 'const int'
Rcpp::Rcerr << "Gene " << g.first << " found no support with " << g.second.size() << " cell types"<< std::endl;
^
eliasFano.cpp: In member function 'long int EliasFanoDB::encodeMatrix(const string&, const NumericMatrix&)':
eliasFano.cpp:518:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto gene_names = Rcpp::as<std::vectorstd::string>(cell_type_genes);
^
eliasFano.cpp:518:8: error: 'gene_names' does not name a type
auto gene_names = Rcpp::as<std::vectorstd::string>(cell_type_genes);
^
eliasFano.cpp:557:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto gene_it = this->genes.insert(std::make_pair(gene_names[gene_row], GeneMeta())).first;
^
eliasFano.cpp:557:10: error: 'gene_it' does not name a type
auto gene_it = this->genes.insert(std::make_pair(gene_names[gene_row], GeneMeta())).first;
^
eliasFano.cpp:559:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto db_entry = this->index.insert(std::make_pair(gene_names[gene_row], GeneContainer())).first;
^
eliasFano.cpp:559:10: error: 'db_entry' does not name a type
auto db_entry = this->index.insert(std::make_pair(gene_names[gene_row], GeneContainer())).first;
^
eliasFano.cpp:565:5: error: 'gene_it' was not declared in this scope
gene_it->second.total_reads += ids.size();
^
eliasFano.cpp:566:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto ef_index = eliasFanoCoding(ids, expression_vector);
^
eliasFano.cpp:566:10: error: 'ef_index' does not name a type
auto ef_index = eliasFanoCoding(ids, expression_vector);
^
eliasFano.cpp:568:9: error: 'ef_index' was not declared in this scope
if (ef_index != -1)
^
eliasFano.cpp:570:7: error: 'db_entry' was not declared in this scope
db_entry->second.insert(std::make_pair(cell_type_id, ef_index));
^
eliasFano.cpp:575:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& cell : current_cells)
^
eliasFano.cpp:575:27: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& cell : current_cells)
^
eliasFano.cpp:577:14: error: request for member 'reads' in 'cell', which is of non-class type 'const int'
if (cell.reads == 0)
^
eliasFano.cpp:581:11: error: 'class EliasFanoDB' has no member named 'cells'
this->cells.insert({CellID(cell_type_id, ++i), cell});
^
eliasFano.cpp:581:24: warning: extended initializer lists only available with -std=c++11 or -std=gnu++11
this->cells.insert({CellID(cell_type_id, ++i), cell});
^
eliasFano.cpp: In member function 'const std::vector<std::basic_string > EliasFanoDB::_getCellTypes(const std::vector<std::basic_string >&) const':
eliasFano.cpp:597:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto cts = this->_getCellTypes();
^
eliasFano.cpp:597:8: error: 'cts' does not name a type
auto cts = this->_getCellTypes();
^
eliasFano.cpp:599:19: error: 'cts' was not declared in this scope
results.reserve(cts.size());
^
eliasFano.cpp:600:3: error: 'copy_if' is not a member of 'std'
std::copy_if(cts.begin(),
^
eliasFano.cpp: In lambda function:
eliasFano.cpp:604:18: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto it = ct.find_first_of(".");
^
eliasFano.cpp:604:23: error: 'it' does not name a type
auto it = ct.find_first_of(".");
^
eliasFano.cpp:605:22: error: 'it' was not declared in this scope
if (it != std::string::npos)
^
eliasFano.cpp: In member function 'const std::vector<std::basic_string > EliasFanoDB::_getCellTypes(const std::vector<std::basic_string >&) const':
eliasFano.cpp:610:16: warning: lambda expressions only available with -std=c++11 or -std=gnu++11
});
^
eliasFano.cpp: In member function 'Rcpp::List EliasFanoDB::geneSupportInCellTypes(const CharacterVector&, const CharacterVector&) const':
eliasFano.cpp:617:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto cell_types = this->_getCellTypes(Rcpp::as<std::vectorstd::string>(datasets_active));
^
eliasFano.cpp:617:8: error: 'cell_types' does not name a type
auto cell_types = this->_getCellTypes(Rcpp::as<std::vectorstd::string>(datasets_active));
^
eliasFano.cpp:618:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto genes = Rcpp::as<std::vectorEliasFanoDB::GeneName>(gene_names);
^
eliasFano.cpp:618:8: error: 'genes' does not name a type
auto genes = Rcpp::as<std::vectorEliasFanoDB::GeneName>(gene_names);
^
eliasFano.cpp:621:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& g : genes)
^
eliasFano.cpp:621:24: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& g : genes)
^
eliasFano.cpp:624:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : cell_types)
^
eliasFano.cpp:624:27: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : cell_types)
^
eliasFano.cpp:624:27: error: 'cell_types' was not declared in this scope
eliasFano.cpp:630:15: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto r = this->ef_data.at(this->index.at(g).at(this->cell_types.at(ct)));
^
eliasFano.cpp:630:20: error: 'r' does not name a type
const auto r = this->ef_data.at(this->index.at(g).at(this->cell_types.at(ct)));
^
eliasFano.cpp:631:16: error: 'r' was not declared in this scope
size = r.getSize();
^
eliasFano.cpp:637:38: error: no matching function for call to 'Rcpp::Vector<13>::push_back(int&, const int&)'
gene_results.push_back(size, ct);
^
eliasFano.cpp:637:38: note: candidates are:
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/Vector.h:52:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:40,
from functions.h:4,
from eliasFano.cpp:10:
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/vector/Vector.h:453:10: note: template void Rcpp::Vector<RTYPE, StoragePolicy>::push_back(const T&) [with T = T; int RTYPE = 13; StoragePolicy = Rcpp::PreserveStorage]
void push_back( const T& object){
^
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/vector/Vector.h:453:10: note: template argument deduction/substitution failed:
eliasFano.cpp:637:38: note: candidate expects 1 argument, 2 provided
gene_results.push_back(size, ct);
^
In file included from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/Vector.h:52:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:40,
from functions.h:4,
from eliasFano.cpp:10:
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/vector/Vector.h:460:10: note: template void Rcpp::Vector<RTYPE, StoragePolicy>::push_back(const T&, const string&) [with T = T; int RTYPE = 13; StoragePolicy = Rcpp::PreserveStorage]
void push_back( const T& object, const std::string& name ){
^
C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/vector/Vector.h:460:10: note: template argument deduction/substitution failed:
eliasFano.cpp:637:38: note: cannot convert 'ct' (type 'const int') to type 'const string& {aka const std::basic_string&}'
gene_results.push_back(size, ct);
^
eliasFano.cpp: In member function 'Rcpp::List EliasFanoDB::total_genes()':
eliasFano.cpp:648:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for(auto & d : index)
^
eliasFano.cpp:648:18: error: range-based 'for' loops are not allowed in C++98 mode
for(auto & d : index)
^
eliasFano.cpp:650:30: error: request for member 'first' in 'd', which is of non-class type 'int'
t.push_back(Rcpp::wrap(d.first));
^
eliasFano.cpp: In member function 'Rcpp::IntegerVector EliasFanoDB::totalCells(const CharacterVector&, const CharacterVector&) const':
eliasFano.cpp:659:71: error: '>>' should be '> >' within a nested template argument list
std::vectorstd::string datasets = Rcpp::as<std::vectorstd::string>(datasets_active);
^
eliasFano.cpp:661:66: error: '>>' should be '> >' within a nested template argument list
std::vectorstd::string str = Rcpp::as<std::vectorstd::string> (genes);
^
eliasFano.cpp:664:3: error: 'unordered_map' is not a member of 'std'
std::unordered_map<CellTypeID, CellTypeName> inv_ct;
^
eliasFano.cpp:664:3: note: suggested alternative:
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tr1/unordered_map:42:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/platform/compiler.h:172,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/r/headers.h:59,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:29,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tr1/unordered_map.h:180:11: note: 'std::tr1::unordered_map'
class unordered_map
^
eliasFano.cpp:664:32: error: expected primary-expression before ',' token
std::unordered_map<CellTypeID, CellTypeName> inv_ct;
^
eliasFano.cpp:664:46: error: expected primary-expression before '>' token
std::unordered_map<CellTypeID, CellTypeName> inv_ct;
^
eliasFano.cpp:664:48: error: 'inv_ct' was not declared in this scope
std::unordered_map<CellTypeID, CellTypeName> inv_ct;
^
eliasFano.cpp:665:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : this->cell_types)
^
eliasFano.cpp:665:25: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : this->cell_types)
^
eliasFano.cpp:665:31: error: 'const class EliasFanoDB' has no member named 'cell_types'
for (auto const& ct : this->cell_types)
^
eliasFano.cpp:667:15: error: request for member 'second' in 'ct', which is of non-class type 'const int'
inv_ct[ct.second] = ct.first;
^
eliasFano.cpp:667:28: error: request for member 'first' in 'ct', which is of non-class type 'const int'
inv_ct[ct.second] = ct.first;
^
eliasFano.cpp:671:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& g : str)
^
eliasFano.cpp:671:24: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& g : str)
^
eliasFano.cpp:673:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto git = this->index.find(g);
^
eliasFano.cpp:673:10: error: 'git' does not name a type
auto git = this->index.find(g);
^
eliasFano.cpp:674:9: error: 'git' was not declared in this scope
if (git != this->index.end())
^
eliasFano.cpp:674:28: error: request for member 'end' in '((const EliasFanoDB*)this)->EliasFanoDB::index', which is of non-class type 'const GeneExpressionDB {aka const int}'
if (git != this->index.end())
^
eliasFano.cpp:676:12: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : git->second)
^
eliasFano.cpp:676:29: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : git->second)
^
eliasFano.cpp:678:48: error: request for member 'first' in 'ct', which is of non-class type 'const int'
const std::string& ct_name = inv_ct[ct.first];
^
eliasFano.cpp:680:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto find_dataset = std::find(datasets.begin(), datasets.end(), ct_dataset);
^
eliasFano.cpp:680:14: error: 'find_dataset' does not name a type
auto find_dataset = std::find(datasets.begin(), datasets.end(), ct_dataset);
^
eliasFano.cpp:682:13: error: 'find_dataset' was not declared in this scope
if (find_dataset == datasets.end())
^
eliasFano.cpp:686:34: error: request for member 'second' in 'ct', which is of non-class type 'const int'
t[i] += this->ef_data[ct.second].getSize();
^
eliasFano.cpp:671:20: warning: unused variable 'g' [-Wunused-variable]
for (auto const& g : str)
^
eliasFano.cpp: At global scope:
eliasFano.cpp:696:14: error: 'CellTypeIndex' in 'class EliasFanoDB' does not name a type
EliasFanoDB::CellTypeIndex EliasFanoDB::getCellTypeIDs(const std::setstd::string& datasets) const
^
eliasFano.cpp: In member function 'int EliasFanoDB::getTotalCells(const CharacterVector&) const':
eliasFano.cpp:725:3: error: 'CellTypeIndex' was not declared in this scope
CellTypeIndex active_cell_types = getCellTypeIDs(act_set);
^
eliasFano.cpp:727:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : active_cell_types)
^
eliasFano.cpp:727:25: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : active_cell_types)
^
eliasFano.cpp:727:25: error: 'active_cell_types' was not declared in this scope
eliasFano.cpp:729:57: error: request for member 'second' in 'ct', which is of non-class type 'const int'
total_number_of_cells += this->inverse_cell_type[ct.second].total_cells;
^
eliasFano.cpp: In member function 'int EliasFanoDB::numberOfCellTypes(const CharacterVector&) const':
eliasFano.cpp:738:3: error: 'CellTypeIndex' was not declared in this scope
CellTypeIndex active_cell_types = getCellTypeIDs(act_set);
^
eliasFano.cpp:740:10: error: 'active_cell_types' was not declared in this scope
return active_cell_types.size();
^
eliasFano.cpp: In member function 'Rcpp::NumericVector EliasFanoDB::getCellTypeSupport(Rcpp::CharacterVector&)':
eliasFano.cpp:746:66: error: '>>' should be '> >' within a nested template argument list
std::vectorstd::string cts = Rcpp::as<std::vectorstd::string>(cell_types);
^
eliasFano.cpp:749:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : cts)
^
eliasFano.cpp:749:25: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : cts)
^
eliasFano.cpp:752:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto cit = this->cell_types.find(ct);
^
eliasFano.cpp:752:10: error: 'cit' does not name a type
auto cit = this->cell_types.find(ct);
^
eliasFano.cpp:753:8: error: 'cit' was not declared in this scope
if(cit != this->cell_types.end())
^
eliasFano.cpp:753:21: error: 'class EliasFanoDB' has no member named 'cell_types'
if(cit != this->cell_types.end())
^
eliasFano.cpp:749:20: warning: unused variable 'ct' [-Wunused-variable]
for (auto const& ct : cts)
^
eliasFano.cpp: In member function 'Rcpp::List EliasFanoDB::queryGenes(const CharacterVector&, const CharacterVector&)':
eliasFano.cpp:778:15: error: request for member 'find' in '((EliasFanoDB*)this)->EliasFanoDB::index', which is of non-class type 'EliasFanoDB::GeneExpressionDB {aka int}'
if (index.find(gene_name) == index.end())
^
eliasFano.cpp:778:40: error: request for member 'end' in '((EliasFanoDB*)this)->EliasFanoDB::index', which is of non-class type 'EliasFanoDB::GeneExpressionDB {aka int}'
if (index.find(gene_name) == index.end())
^
eliasFano.cpp:784:73: error: '>>' should be '> >' within a nested template argument list
std::vectorstd::string datasets = Rcpp::as<std::vectorstd::string>(datasets_active);
^
eliasFano.cpp:785:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto& gene_meta = index[gene_name];
^
eliasFano.cpp:785:34: error: no match for 'operator[]' (operand types are 'EliasFanoDB::GeneExpressionDB {aka int}' and 'std::string {aka std::basic_string}')
const auto& gene_meta = index[gene_name];
^
eliasFano.cpp:786:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& dat : gene_meta)
^
eliasFano.cpp:786:28: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& dat : gene_meta)
^
eliasFano.cpp:788:64: error: request for member 'first' in 'dat', which is of non-class type 'const int'
CellType current_cell_type = this->inverse_cell_type[dat.first];
^
eliasFano.cpp:791:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto ct_find = std::find(datasets.begin(), datasets.end(), dataset);
^
eliasFano.cpp:791:12: error: 'ct_find' does not name a type
auto ct_find = std::find(datasets.begin(), datasets.end(), dataset);
^
eliasFano.cpp:793:11: error: 'ct_find' was not declared in this scope
if (ct_find == datasets.end())
^
eliasFano.cpp:797:60: error: request for member 'second' in 'dat', which is of non-class type 'const int'
std::vector ids = eliasFanoDecoding(ef_data[dat.second]);
^
eliasFano.cpp: In member function 'size_t EliasFanoDB::dataMemoryFootprint()':
eliasFano.cpp:810:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for(auto & d : ef_data)
^
eliasFano.cpp:810:18: error: range-based 'for' loops are not allowed in C++98 mode
for(auto & d : ef_data)
^
eliasFano.cpp:812:21: error: request for member 'H' in 'd', which is of non-class type 'int'
bytes += int((d.H.size() / 8) + 1);
^
eliasFano.cpp:813:21: error: request for member 'L' in 'd', which is of non-class type 'int'
bytes += int((d.L.size() / 8) + 1);
^
eliasFano.cpp:814:21: error: request for member 'expr' in 'd', which is of non-class type 'int'
bytes += int((d.expr.quantile.size() / 8) + 12);
^
eliasFano.cpp: In member function 'size_t EliasFanoDB::quantizationMemoryFootprint()':
eliasFano.cpp:824:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto & d : ef_data)
^
eliasFano.cpp:824:19: error: range-based 'for' loops are not allowed in C++98 mode
for (auto & d : ef_data)
^
eliasFano.cpp:826:21: error: request for member 'expr' in 'd', which is of non-class type 'int'
bytes += int((d.expr.quantile.size() / 8) + 12);
^
eliasFano.cpp: In member function 'size_t EliasFanoDB::dbMemoryFootprint()':
eliasFano.cpp:841:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& d : index)
^
eliasFano.cpp:841:24: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& d : index)
^
eliasFano.cpp:844:16: error: request for member 'first' in 'd', which is of non-class type 'const int'
bytes += d.first.size() * 2;
^
eliasFano.cpp:845:16: error: request for member 'second' in 'd', which is of non-class type 'const int'
bytes += d.second.size() * 4;
^
eliasFano.cpp:848:18: error: request for member 'size' in '((EliasFanoDB*)this)->EliasFanoDB::index', which is of non-class type 'EliasFanoDB::GeneExpressionDB {aka int}'
bytes += index.size() * (sizeof(GeneMeta) + 8);
^
eliasFano.cpp:851:12: error: 'cells' was not declared in this scope
bytes += cells.size() * (sizeof(CellID) + sizeof(CellMeta) + 4);
^
eliasFano.cpp:854:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& c : cell_types)
^
eliasFano.cpp:854:24: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& c : cell_types)
^
eliasFano.cpp:854:24: error: 'cell_types' was not declared in this scope
eliasFano.cpp:856:17: error: request for member 'first' in 'c', which is of non-class type 'const int'
bytes += (c.first.size()2) + 4 + sizeof(CellType);
^
eliasFano.cpp: In member function 'Rcpp::CharacterVector EliasFanoDB::getGenesInDB()':
eliasFano.cpp:869:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for(auto const& g : this->genes)
^
eliasFano.cpp:869:23: error: range-based 'for' loops are not allowed in C++98 mode
for(auto const& g : this->genes)
^
eliasFano.cpp:871:28: error: request for member 'first' in 'g', which is of non-class type 'const int'
gene_names.push_back(g.first);
^
eliasFano.cpp: In member function 'Rcpp::List EliasFanoDB::findCellTypes(const CharacterVector&, const CharacterVector&)':
eliasFano.cpp:881:3: error: 'unordered_map' is not a member of 'std'
std::unordered_map<CellTypeID, std::setstd::string > cell_types;
^
eliasFano.cpp:881:3: note: suggested alternative:
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tr1/unordered_map:42:0,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/platform/compiler.h:172,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp/r/headers.h:59,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/RcppCommon.h:29,
from C:/Program Files/R/R-3.5.0/library/Rcpp/include/Rcpp.h:27,
from functions.h:4,
from eliasFano.cpp:10:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/tr1/unordered_map.h:180:11: note: 'std::tr1::unordered_map'
class unordered_map
^
eliasFano.cpp:881:32: error: expected primary-expression before ',' token
std::unordered_map<CellTypeID, std::setstd::string > cell_types;
^
eliasFano.cpp:881:56: error: expected primary-expression before '>' token
std::unordered_map<CellTypeID, std::setstd::string > cell_types;
^
eliasFano.cpp:881:58: error: 'cell_types' was not declared in this scope
std::unordered_map<CellTypeID, std::setstd::string > cell_types;
^
eliasFano.cpp:884:71: error: '>>' should be '> >' within a nested template argument list
std::vectorstd::string datasets = Rcpp::as<std::vectorstd::string>(datasets_active);
^
eliasFano.cpp:892:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto db_it = index.find(gene_name);
^
eliasFano.cpp:892:10: error: 'db_it' does not name a type
auto db_it = index.find(gene_name);
^
eliasFano.cpp:893:9: error: 'db_it' was not declared in this scope
if (db_it == index.end())
^
eliasFano.cpp:893:24: error: request for member 'end' in '((EliasFanoDB)this)->EliasFanoDB::index', which is of non-class type 'EliasFanoDB::GeneExpressionDB {aka int}'
if (db_it == index.end())
^
eliasFano.cpp:900:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct_it : db_it->second)
^
eliasFano.cpp:900:30: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct_it : db_it->second)
^
eliasFano.cpp:900:30: error: 'db_it' was not declared in this scope
eliasFano.cpp:902:51: error: request for member 'first' in 'ct_it', which is of non-class type 'const int'
CellType ct = this->inverse_cell_type[ct_it.first];
^
eliasFano.cpp:906:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto find_dataset = std::find(datasets.begin(), datasets.end(), ct_dataset);
^
eliasFano.cpp:906:12: error: 'find_dataset' does not name a type
auto find_dataset = std::find(datasets.begin(), datasets.end(), ct_dataset);
^
eliasFano.cpp:908:11: error: 'find_dataset' was not declared in this scope
if (find_dataset == datasets.end())
^
eliasFano.cpp:913:33: error: request for member 'first' in 'ct_it', which is of non-class type 'const int'
if (cell_types.find(ct_it.first) == cell_types.end())
^
eliasFano.cpp:915:26: error: request for member 'first' in 'ct_it', which is of non-class type 'const int'
cell_types[ct_it.first] = std::setstd::string();
^
eliasFano.cpp:917:24: error: request for member 'first' in 'ct_it', which is of non-class type 'const int'
cell_types[ct_it.first].insert(gene_name);
^
eliasFano.cpp:925:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : cell_types)
^
eliasFano.cpp:925:25: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : cell_types)
^
eliasFano.cpp:927:12: error: request for member 'second' in 'ct', which is of non-class type 'const int'
if (ct.second.size() != genes.size())
^
eliasFano.cpp:932:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto g_it = ct.second.begin();
^
eliasFano.cpp:932:10: error: 'g_it' does not name a type
auto g_it = ct.second.begin();
^
eliasFano.cpp:933:66: error: 'g_it' was not declared in this scope
std::vector ef = eliasFanoDecoding(this->ef_data[index[g_it][ct.first]]);
^
eliasFano.cpp:933:75: error: request for member 'first' in 'ct', which is of non-class type 'const int'
std::vector ef = eliasFanoDecoding(this->ef_data[index[g_it][ct.first]]);
^
eliasFano.cpp:935:29: error: request for member 'second' in 'ct', which is of non-class type 'const int'
for (++g_it; g_it != ct.second.end();++g_it)
^
eliasFano.cpp:937:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto cells = eliasFanoDecoding(this->ef_data[index[g_it][ct.first]]);
^
eliasFano.cpp:937:12: error: 'cells' does not name a type
auto cells = eliasFanoDecoding(this->ef_data[index[g_it][ct.first]]);
^
eliasFano.cpp:942:29: error: 'cells' was not declared in this scope
cells.begin(),
^
eliasFano.cpp:954:36: error: request for member 'first' in 'ct', which is of non-class type 'const int'
t[this->inverse_cell_type[ct.first].name] = Rcpp::wrap(ef);
^
eliasFano.cpp: In member function 'Rcpp::DataFrame EliasFanoDB::findMarkerGenes(const CharacterVector&, Rcpp::CharacterVector, unsigned int, bool)':
eliasFano.cpp:976:40: error: 'Transaction' was not declared in this scope
std::map<CellTypeName, std::map<int, Transaction> > cells;
^
eliasFano.cpp:976:51: error: template argument 2 is invalid
std::map<CellTypeName, std::map<int, Transaction> > cells;
^
eliasFano.cpp:976:51: error: template argument 4 is invalid
eliasFano.cpp:976:53: error: template argument 2 is invalid
std::map<CellTypeName, std::map<int, Transaction> > cells;
^
eliasFano.cpp:976:53: error: template argument 4 is invalid
eliasFano.cpp:976:60: error: invalid type in declaration before ';' token
std::map<CellTypeName, std::map<int, Transaction> > cells;
^
eliasFano.cpp:984:79: error: '>>' should be '> >' within a nested template argument list
const std::vectorstd::string gene_names = Rcpp::as<std::vectorstd::string>(genes_results.names());
^
eliasFano.cpp:985:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& gene_name : gene_names)
^
eliasFano.cpp:985:32: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& gene_name : gene_names)
^
eliasFano.cpp:990:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& _ct : cell_type_names)
^
eliasFano.cpp:990:28: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& _ct : cell_type_names)
^
eliasFano.cpp:992:13: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto ct = Rcpp::asstd::string(_ct);
^
eliasFano.cpp:992:18: error: 'ct' does not name a type
const auto ct = Rcpp::asstd::string(_ct);
^
eliasFano.cpp:994:17: error: request for member 'find' in 'cells', which is of non-class type 'int'
if (cells.find(ct) == cells.end())
^
eliasFano.cpp:994:22: error: 'ct' was not declared in this scope
if (cells.find(ct) == cells.end())
^
eliasFano.cpp:994:35: error: request for member 'end' in 'cells', which is of non-class type 'int'
if (cells.find(ct) == cells.end())
^
eliasFano.cpp:996:46: error: type/value mismatch at argument 2 in template parameter list for 'template<class _Key, class _Tp, class _Compare, class _Alloc> class std::map'
cells[ct] = std::map<int, Transaction>();
^
eliasFano.cpp:996:46: error: expected a type, got 'Transaction'
eliasFano.cpp:996:46: error: template argument 4 is invalid
eliasFano.cpp:999:87: error: 'ct' was not declared in this scope
std::vector ids = Rcpp::as<std::vector >(gene_hits[ct]);
^
eliasFano.cpp:1000:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto& cell_index = cells[ct];
^
eliasFano.cpp:1002:12: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& id : ids)
^
eliasFano.cpp:1002:29: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& id : ids)
^
eliasFano.cpp:1005:24: error: request for member 'find' in 'cell_index', which is of non-class type 'int'
if (cell_index.find(id) == cell_index.end())
^
eliasFano.cpp:1005:47: error: request for member 'end' in 'cell_index', which is of non-class type 'int'
if (cell_index.find(id) == cell_index.end())
^
eliasFano.cpp:1008:24: error: invalid types 'int[const int]' for array subscript
cell_index[id] = Transaction();
^
eliasFano.cpp:1012:22: error: invalid types 'int[const int]' for array subscript
cell_index[id].push_back(gene_name);
^
eliasFano.cpp:990:22: warning: unused variable '_ct' [-Wunused-variable]
for (auto const& _ct : cell_type_names)
^
eliasFano.cpp:1020:26: error: type/value mismatch at argument 1 in template parameter list for 'template<class _Tp, class _Alloc> class std::vector'
std::vector transactions;
^
eliasFano.cpp:1020:26: error: expected a type, got 'Transaction'
eliasFano.cpp:1020:26: error: template argument 2 is invalid
eliasFano.cpp:1020:40: error: invalid type in declaration before ';' token
std::vector transactions;
^
eliasFano.cpp:1021:16: error: request for member 'reserve' in 'transactions', which is of non-class type 'int'
transactions.reserve(cells_present);
^
eliasFano.cpp:1022:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto & ct : cells)
^
eliasFano.cpp:1022:20: error: range-based 'for' loops are not allowed in C++98 mode
for (auto & ct : cells)
^
eliasFano.cpp:1024:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto & cl : ct.second)
^
eliasFano.cpp:1024:22: error: range-based 'for' loops are not allowed in C++98 mode
for (auto & cl : ct.second)
^
eliasFano.cpp:1024:25: error: request for member 'second' in 'ct', which is of non-class type 'int'
for (auto & cl : ct.second)
^
eliasFano.cpp:1028:14: error: request for member 'second' in 'cl', which is of non-class type 'int'
if (cl.second.size() != 1)
^
eliasFano.cpp:1030:22: error: request for member 'push_back' in 'transactions', which is of non-class type 'int'
transactions.push_back(std::vectorstd::string(cl.second.begin(), cl.second.end()));
^
eliasFano.cpp:1030:60: error: request for member 'second' in 'cl', which is of non-class type 'int'
transactions.push_back(std::vectorstd::string(cl.second.begin(), cl.second.end()));
^
eliasFano.cpp:1030:79: error: request for member 'second' in 'cl', which is of non-class type 'int'
transactions.push_back(std::vectorstd::string(cl.second.begin(), cl.second.end()));
^
eliasFano.cpp:1035:31: error: request for member 'size' in 'transactions', which is of non-class type 'int'
Rcpp::Rcerr << transactions.size() << " transactions" << std::endl;
^
eliasFano.cpp:1042:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& v : qs.genes)
^
eliasFano.cpp:1042:24: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& v : qs.genes)
^
eliasFano.cpp:1044:25: error: request for member 'second' in 'v', which is of non-class type 'const int'
cutoffs.push_back(v.second.cartesian_product_sets);
^
eliasFano.cpp:1051:22: warning: extended initializer lists only available with -std=c++11 or -std=gnu++11
const FPTree fptree{transactions, min_support_cutoff};
^
eliasFano.cpp:1051:55: error: in C++98 'fptree' must be initialized by constructor, not by '{...}'
const FPTree fptree{transactions, min_support_cutoff};
^
eliasFano.cpp:1051:55: warning: narrowing conversion of 'min_support_cutoff' from 'unsigned int' to 'int' inside { } is ill-formed in C++11 [-Wnarrowing]
eliasFano.cpp:1052:18: error: 'Pattern' was not declared in this scope
const std::set patterns = fptree_growth(fptree);
^
eliasFano.cpp:1052:25: error: template argument 1 is invalid
const std::set patterns = fptree_growth(fptree);
^
eliasFano.cpp:1052:25: error: template argument 2 is invalid
eliasFano.cpp:1052:25: error: template argument 3 is invalid
eliasFano.cpp:1052:36: error: invalid type in declaration before '=' token
const std::set patterns = fptree_growth(fptree);
^
eliasFano.cpp:1053:39: error: request for member 'size' in 'patterns', which is of non-class type 'const int'
Rcpp::Rcerr << "Found " << patterns.size() << " geneset patterns " << std::endl;
^
eliasFano.cpp:1058:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& item : patterns)
^
eliasFano.cpp:1058:27: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& item : patterns)
^
eliasFano.cpp:1063:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto& gene_set = item.first;
^
eliasFano.cpp:1063:33: error: request for member 'first' in 'item', which is of non-class type 'const int'
const auto& gene_set = item.first;
^
eliasFano.cpp:1066:18: error: request for member 'size' in 'gene_set', which is of non-class type 'const int'
if (gene_set.size() < 2)
^
eliasFano.cpp:1071:52: error: 'Item' was not declared in this scope
std::string view_string = str_join(std::vector(gene_set.begin(), gene_set.end()), ",");
^
eliasFano.cpp:1071:56: error: template argument 1 is invalid
std::string view_string = str_join(std::vector(gene_set.begin(), gene_set.end()), ",");
^
eliasFano.cpp:1071:56: error: template argument 2 is invalid
eliasFano.cpp:1071:67: error: request for member 'begin' in 'gene_set', which is of non-class type 'const int'
std::string view_string = str_join(std::vector(gene_set.begin(), gene_set.end()), ",");
^
eliasFano.cpp:1071:85: error: request for member 'end' in 'gene_set', which is of non-class type 'const int'
std::string view_string = str_join(std::vector(gene_set.begin(), gene_set.end()), ",");
^
eliasFano.cpp:1078:43: error: request for member 'second' in 'item', which is of non-class type 'const int'
query_cell_cardinality.push_back(item.second);
^
eliasFano.cpp:1083:34: error: no matching function for call to 'QueryScore::cell_tfidf(EliasFanoDB&, const int&)'
qs.cell_tfidf(this, gene_set);
^
eliasFano.cpp:1083:34: note: candidate is:
eliasFano.cpp:243:6: note: void QueryScore::cell_tfidf(const EliasFanoDB&, const std::set<std::basic_string >&)
void QueryScore::cell_tfidf(const EliasFanoDB& db, const std::setstd::string& gene_set)
^
eliasFano.cpp:243:6: note: no known conversion for argument 2 from 'const int' to 'const std::set<std::basic_string >&'
eliasFano.cpp:1090:66: error: no matching function for call to 'QueryScore::calculate_cell_types(const int&)'
int available_cell_types = qs.calculate_cell_types(gene_set);
^
eliasFano.cpp:1090:66: note: candidate is:
eliasFano.cpp:259:5: note: int QueryScore::calculate_cell_types(const std::set<std::basic_string >&)
int QueryScore::calculate_cell_types(const std::setstd::string&gene_set)
^
eliasFano.cpp:259:5: note: no known conversion for argument 1 from 'const int' to 'const std::set<std::basic_string >&'
eliasFano.cpp:1099:47: error: request for member 'size' in 'gene_set', which is of non-class type 'const int'
query_gene_cardinality.push_back(gene_set.size());
^
eliasFano.cpp: In member function 'const std::set<std::basic_string > EliasFanoDB::_getValidCellTypes(std::vector<std::basic_string >) const':
eliasFano.cpp:1148:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for(auto const& ct : cts_not_found)
^
eliasFano.cpp:1148:26: error: range-based 'for' loops are not allowed in C++98 mode
for(auto const& ct : cts_not_found)
^
eliasFano.cpp: In member function 'Rcpp::DataFrame EliasFanoDB::findCellTypeMarkers(const CharacterVector&, const CharacterVector&)':
eliasFano.cpp:1163:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& g : this->genes)
^
eliasFano.cpp:1163:24: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& g : this->genes)
^
eliasFano.cpp:1165:26: error: request for member 'first' in 'g', which is of non-class type 'const int'
gene_set.push_back(g.first);
^
eliasFano.cpp: In member function 'Rcpp::DataFrame EliasFanoDB::_findCellTypeMarkers(const CharacterVector&, const CharacterVector&, const std::vector<std::basic_string >&)':
eliasFano.cpp:1181:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : cts)
^
eliasFano.cpp:1181:25: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : cts)
^
eliasFano.cpp:1183:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto marker_genes = this->_cellTypeScore(ct, bk_cts, gene_set);
^
eliasFano.cpp:1183:10: error: 'marker_genes' does not name a type
auto marker_genes = this->_cellTypeScore(ct, bk_cts, gene_set);
^
eliasFano.cpp:1184:9: error: 'marker_genes' was not declared in this scope
if (marker_genes.empty())
^
eliasFano.cpp:1190:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto& t : marker_genes)
^
eliasFano.cpp:1190:20: error: range-based 'for' loops are not allowed in C++98 mode
for (auto& t : marker_genes)
^
eliasFano.cpp:1190:20: error: 'marker_genes' was not declared in this scope
eliasFano.cpp:1192:37: error: request for member 'second' in 't', which is of non-class type 'int'
const CellTypeMarker& ctm = t.second;
^
eliasFano.cpp:1193:25: error: request for member 'first' in 't', which is of non-class type 'int'
genes.push_back(t.first);
^
eliasFano.cpp:1194:32: error: invalid user-defined conversion from 'const int' to 'const value_type& {aka const std::basic_string&}' [-fpermissive]
df_cell_type.push_back(ct);
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:53:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: candidate is: std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]
basic_string<_CharT, _Traits, _Alloc>::
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: no known conversion for argument 1 from 'const int' to 'const char'
eliasFano.cpp:1194:32: error: invalid conversion from 'int' to 'const char' [-fpermissive]
df_cell_type.push_back(ct);
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:53:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: initializing argument 1 of 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]'
basic_string<_CharT, _Traits, _Alloc>::
^
eliasFano.cpp: In member function 'Rcpp::DataFrame EliasFanoDB::evaluateCellTypeMarkers(const CharacterVector&, const CharacterVector&, const CharacterVector&)':
eliasFano.cpp:1223:84: error: '>>' should be '> >' within a nested template argument list
return _findCellTypeMarkers(cell_types, background, Rcpp::as<std::vector>(gene_set));
^
eliasFano.cpp: In member function 'std::map<std::basic_string, CellTypeMarker> EliasFanoDB::_cellTypeScore(const string&, const std::vector<std::basic_string >&, const std::vector<std::basic_string >&) const':
eliasFano.cpp:1230:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto ct_it = this->cell_types.find(cell_type);
^
eliasFano.cpp:1230:8: error: 'ct_it' does not name a type
auto ct_it = this->cell_types.find(cell_type);
^
eliasFano.cpp:1231:8: error: 'ct_it' was not declared in this scope
if ( ct_it == this->cell_types.end())
^
eliasFano.cpp:1231:23: error: 'const class EliasFanoDB' has no member named 'cell_types'
if ( ct_it == this->cell_types.end())
^
eliasFano.cpp:1237:35: error: 'ct_it' was not declared in this scope
const CellTypeID cell_type_id = ct_it->second;
^
eliasFano.cpp:1239:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto active_cell_types = this->_getValidCellTypes(universe);
^
eliasFano.cpp:1239:14: error: 'active_cell_types' does not name a type
const auto active_cell_types = this->_getValidCellTypes(universe);
^
eliasFano.cpp:1243:9: error: 'CellTypeIndex' does not name a type
const CellTypeIndex& cts_index = this->cell_types;
^
eliasFano.cpp:1244:47: error: 'active_cell_types' was not declared in this scope
const int act_total_cells = std::accumulate(active_cell_types.begin(),
^
eliasFano.cpp:1247:59: error: 'cts_index' was not declared in this scope
[&all_cts, &cts_index](const int& sum, const CellTypeName& name){
^
eliasFano.cpp: In lambda function:
eliasFano.cpp:1248:55: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto ct_id = cts_index.find(name);
^
eliasFano.cpp:1248:60: error: 'ct_id' does not name a type
const auto ct_id = cts_index.find(name);
^
eliasFano.cpp:1249:70: error: 'ct_id' was not declared in this scope
return sum + all_cts[ct_id->second].total_cells;
^
eliasFano.cpp: In member function 'std::map<std::basic_string, CellTypeMarker> EliasFanoDB::_cellTypeScore(const string&, const std::vector<std::basic_string >&, const std::vector<std::basic_string >&) const':
eliasFano.cpp:1250:47: warning: lambda expressions only available with -std=c++11 or -std=gnu++11
});
^
eliasFano.cpp:1255:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& gene_name : gene_names)
^
eliasFano.cpp:1255:32: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& gene_name : gene_names)
^
eliasFano.cpp:1257:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto index_it = this->index.find(gene_name);
^
eliasFano.cpp:1257:16: error: 'index_it' does not name a type
const auto index_it = this->index.find(gene_name);
^
eliasFano.cpp:1258:9: error: 'index_it' was not declared in this scope
if (index_it == this->index.end())
^
eliasFano.cpp:1258:33: error: request for member 'end' in '((const EliasFanoDB)this)->EliasFanoDB::index', which is of non-class type 'const GeneExpressionDB {aka const int}'
if (index_it == this->index.end())
^
eliasFano.cpp:1264:11: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto& gene_entry = index_it;
^
eliasFano.cpp:1264:31: error: 'index_it' was not declared in this scope
const auto& gene_entry = index_it;
^
eliasFano.cpp:1266:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto ctm = gene_entry.second.find(cell_type_id);
^
eliasFano.cpp:1266:10: error: 'ctm' does not name a type
auto ctm = gene_entry.second.find(cell_type_id);
^
eliasFano.cpp:1267:9: error: 'ctm' was not declared in this scope
if (ctm == gene_entry.second.end())
^
eliasFano.cpp:1267:27: error: request for member 'second' in 'gene_entry', which is of non-class type 'const int'
if (ctm == gene_entry.second.end())
^
eliasFano.cpp:1272:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto dit = scores.insert(std::make_pair(gene_entry.first, ctm_template));
^
eliasFano.cpp:1272:10: error: 'dit' does not name a type
auto dit = scores.insert(std::make_pair(gene_entry.first, ctm_template));
^
eliasFano.cpp:1273:38: error: 'dit' was not declared in this scope
CellTypeMarker& gene_ctm_score = dit.first->second;
^
eliasFano.cpp:1275:45: error: 'ctm' was not declared in this scope
const EliasFano& ex_vec = this->ef_data[ctm->second];
^
eliasFano.cpp:1280:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : gene_entry.second)
^
eliasFano.cpp:1280:27: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : gene_entry.second)
^
eliasFano.cpp:1280:38: error: request for member 'second' in 'gene_entry', which is of non-class type 'const int'
for (auto const& ct : gene_entry.second)
^
eliasFano.cpp:1282:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto bct_it = active_cell_types.find(all_cts[ct.first].name);
^
eliasFano.cpp:1282:12: error: 'bct_it' does not name a type
auto bct_it = active_cell_types.find(all_cts[ct.first].name);
^
eliasFano.cpp:1284:12: error: 'bct_it' was not declared in this scope
if ( bct_it == active_cell_types.end())
^
eliasFano.cpp:1294:46: error: request for member 'second' in 'ct', which is of non-class type 'const int'
int bkg_cell_number = this->ef_data[ct.second].getSize();
^
eliasFano.cpp:1253:18: warning: unused variable 'ctm_template' [-Wunused-variable]
CellTypeMarker ctm_template = {0, 0, 0, 0};
^
eliasFano.cpp: In member function 'const std::vector<std::basic_string > EliasFanoDB::_getCellTypes() const':
eliasFano.cpp:1313:21: error: 'const class EliasFanoDB' has no member named 'cell_types'
cts.reserve(this->cell_types.size());
^
eliasFano.cpp:1314:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : this->inverse_cell_type)
^
eliasFano.cpp:1314:25: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : this->inverse_cell_type)
^
eliasFano.cpp:1316:22: error: request for member 'name' in 'ct', which is of non-class type 'const int'
cts.push_back(ct.name);
^
eliasFano.cpp: At global scope:
eliasFano.cpp:1321:38: error: '>>' should be '> >' within a nested template argument list
std::map<std::string, std::vector> EliasFanoDB::intersect_cells(std::setstd::string gene_set, Rcpp::List genes_results) const
^
eliasFano.cpp: In member function 'std::map<std::basic_string, std::vector > EliasFanoDB::intersect_cells(std::set<std::basic_string >, Rcpp::List) const':
eliasFano.cpp:1327:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto git = gene_set.begin();
^
eliasFano.cpp:1327:8: error: 'git' does not name a type
auto git = gene_set.begin();
^
eliasFano.cpp:1329:49: error: 'git' was not declared in this scope
const Rcpp::List& first_gene = genes_results[git];
^
eliasFano.cpp:1331:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : initial_cell_types)
^
eliasFano.cpp:1331:25: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : initial_cell_types)
^
eliasFano.cpp:1333:14: error: invalid user-defined conversion from 'const int' to 'const key_type& {aka const std::basic_string&}' [-fpermissive]
ct_map[ct] = Rcpp::as< std::vector >(first_gene[ct]);
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:53:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: candidate is: std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]
basic_string<_CharT, _Traits, _Alloc>::
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: no known conversion for argument 1 from 'const int' to 'const char'
eliasFano.cpp:1333:14: error: invalid conversion from 'int' to 'const char' [-fpermissive]
ct_map[ct] = Rcpp::as< std::vector >(first_gene[ct]);
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/string:53:0,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/locale_classes.h:40,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/ios_base.h:41,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ios:42,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/ostream:38,
from C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/iterator:64,
from eliasFano.cpp:2:
C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/bits/basic_string.tcc:212:5: note: initializing argument 1 of 'std::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]'
basic_string<_CharT, _Traits, _Alloc>::
^
eliasFano.cpp:1342:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : ct_map)
^
eliasFano.cpp:1342:27: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : ct_map)
^
eliasFano.cpp:1344:41: error: request for member 'first' in 'ct', which is of non-class type 'const int'
cell_types_in_ct_map.push_back(ct.first);
^
eliasFano.cpp:1359:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for(auto m_it = ct_map.begin(); m_it != ct_map.end();)
^
eliasFano.cpp:1359:14: error: 'm_it' does not name a type
for(auto m_it = ct_map.begin(); m_it != ct_map.end();)
^
eliasFano.cpp:1359:37: error: expected ';' before 'm_it'
for(auto m_it = ct_map.begin(); m_it != ct_map.end();)
^
eliasFano.cpp:1359:37: error: 'm_it' was not declared in this scope
eliasFano.cpp:1361:7: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto f_it = std::find(ct_intersection.begin(),ct_intersection.end(), m_it->first);
^
eliasFano.cpp:1361:12: error: 'f_it' does not name a type
auto f_it = std::find(ct_intersection.begin(),ct_intersection.end(), m_it->first);
^
eliasFano.cpp:1362:11: error: 'f_it' was not declared in this scope
if (f_it == ct_intersection.end())
^
eliasFano.cpp: In member function 'int EliasFanoDB::dbSize()':
eliasFano.cpp:1380:24: error: request for member 'size' in '((EliasFanoDB*)this)->EliasFanoDB::index', which is of non-class type 'EliasFanoDB::GeneExpressionDB {aka int}'
Rcpp::Rcout << index.size() << "genes in the DB" << std::endl;
^
eliasFano.cpp: In member function 'int EliasFanoDB::insertNewCellType(const CellType&)':
eliasFano.cpp:1398:3: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto ct_it = this->cell_types.insert(std::make_pair(cell_type.name, this->cell_types.size()));
^
eliasFano.cpp:1398:8: error: 'ct_it' does not name a type
auto ct_it = this->cell_types.insert(std::make_pair(cell_type.name, this->cell_types.size()));
^
eliasFano.cpp:1400:11: error: 'ct_it' was not declared in this scope
if (not ct_it.second)
^
eliasFano.cpp:1410:10: error: 'ct_it' was not declared in this scope
return ct_it.first->second;
^
eliasFano.cpp: In member function 'int EliasFanoDB::mergeDB(const EliasFanoDB&)':
eliasFano.cpp:1421:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& ct : extdb.inverse_cell_type)
^
eliasFano.cpp:1421:25: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& ct : extdb.inverse_cell_type)
^
eliasFano.cpp:1423:25: error: no matching function for call to 'EliasFanoDB::insertNewCellType(const int&)'
insertNewCellType(ct);
^
eliasFano.cpp:1423:25: note: candidate is:
eliasFano.cpp:1396:5: note: int EliasFanoDB::insertNewCellType(const CellType&)
int EliasFanoDB::insertNewCellType(const CellType& cell_type)
^
eliasFano.cpp:1396:5: note: no known conversion for argument 1 from 'const int' to 'const CellType&'
eliasFano.cpp:1427:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for ( auto& gene: extdb.index)
^
eliasFano.cpp:1427:21: error: range-based 'for' loops are not allowed in C++98 mode
for ( auto& gene: extdb.index)
^
eliasFano.cpp:1430:5: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
auto gene_it = this->genes.insert({gene.first, extdb.genes[gene.first]});
^
eliasFano.cpp:1430:10: error: 'gene_it' does not name a type
auto gene_it = this->genes.insert({gene.first, extdb.genes[gene.first]});
^
eliasFano.cpp:1430:76: error: expected primary-expression before ')' token
auto gene_it = this->genes.insert({gene.first, extdb.genes[gene.first]});
^
eliasFano.cpp:1432:12: error: 'gene_it' was not declared in this scope
if(not gene_it.second)
^
eliasFano.cpp:1434:52: error: request for member 'first' in 'gene', which is of non-class type 'int'
gene_it.first->second.merge(extdb.genes[gene.first]);
^
eliasFano.cpp:1437:10: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto& ct : gene.second)
^
eliasFano.cpp:1437:21: error: range-based 'for' loops are not allowed in C++98 mode
for (auto& ct : gene.second)
^
eliasFano.cpp:1437:26: error: request for member 'second' in 'gene', which is of non-class type 'int'
for (auto& ct : gene.second)
^
eliasFano.cpp:1441:42: error: request for member 'second' in 'ct', which is of non-class type 'int'
ef_data.push_back(extdb.ef_data[ct.second]);
^
eliasFano.cpp:1443:32: error: 'class EliasFanoDB' has no member named 'cell_types'
int cell_type_id = this->cell_types[extdb.inverse_cell_type[ct.first].name];
^
eliasFano.cpp:1443:70: error: request for member 'first' in 'ct', which is of non-class type 'int'
int cell_type_id = this->cell_types[extdb.inverse_cell_type[ct.first].name];
^
eliasFano.cpp:1444:18: error: request for member 'first' in 'gene', which is of non-class type 'int'
index[gene.first][cell_type_id] = new_id;
^
eliasFano.cpp:1448:8: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
for (auto const& cell : extdb.cells)
^
eliasFano.cpp:1448:27: error: range-based 'for' loops are not allowed in C++98 mode
for (auto const& cell : extdb.cells)
^
eliasFano.cpp:1448:33: error: 'class EliasFanoDB' has no member named 'cells'
for (auto const& cell : extdb.cells)
^
eliasFano.cpp:1451:23: error: request for member 'first' in 'cell', which is of non-class type 'const int'
CellID clone(cell.first);
^
eliasFano.cpp:1454:34: error: 'class EliasFanoDB' has no member named 'cell_types'
int new_cell_type_id = this->cell_types[extdb.inverse_cell_type[old_cell_type_id].name];
^
eliasFano.cpp:1456:11: error: 'class EliasFanoDB' has no member named 'cells'
this->cells.insert({clone, cell.second});
^
eliasFano.cpp:1456:24: warning: extended initializer lists only available with -std=c++11 or -std=gnu++11
this->cells.insert({clone, cell.second});
^
eliasFano.cpp:1456:37: error: request for member 'second' in 'cell', which is of non-class type 'const int'
this->cells.insert({clone, cell.second});
^
eliasFano.cpp: In member function 'Rcpp::List EliasFanoDB::getCellMeta(const string&, const int&) const':
eliasFano.cpp:1467:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto ct_it = this->cell_types.find(ct);
^
eliasFano.cpp:1467:14: error: 'ct_it' does not name a type
const auto ct_it = this->cell_types.find(ct);
^
eliasFano.cpp:1468:20: error: 'ct_it' was not declared in this scope
const CellID cid(ct_it->second, num);
^
eliasFano.cpp:1469:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto cmeta_it = this->cells.find(cid);
^
eliasFano.cpp:1469:14: error: 'cmeta_it' does not name a type
const auto cmeta_it = this->cells.find(cid);
^
eliasFano.cpp:1470:27: error: 'cmeta_it' was not declared in this scope
const CellMeta& cmeta = cmeta_it->second;
^
eliasFano.cpp: In member function 'Rcpp::List EliasFanoDB::getCellTypeMeta(const string&) const':
eliasFano.cpp:1480:9: warning: 'auto' changes meaning in C++11; please remove it [-Wc++0x-compat]
const auto ct_it = this->cell_types.find(ct_name);
^
eliasFano.cpp:1480:14: error: 'ct_it' does not name a type
const auto ct_it = this->cell_types.find(ct_name);
^
eliasFano.cpp:1481:52: error: 'ct_it' was not declared in this scope
const CellType& ctmeta = this->inverse_cell_type[ct_it->second];
^
eliasFano.cpp: In member function 'const CellType& EliasFanoDB::getCellType(const CellTypeName&) const':
eliasFano.cpp:377:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
eliasFano.cpp: In member function 'const EliasFano& EliasFanoDB::getEntry(const GeneName&, const CellTypeName&) const':
eliasFano.cpp:476:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
eliasFano.cpp: In member function 'int EliasFanoDB::numberOfCellTypes(const CharacterVector&) const':
eliasFano.cpp:741:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
eliasFano.cpp: In member function 'int EliasFanoDB::insertNewCellType(const CellType&)':
eliasFano.cpp:1411:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
make: *** [C:/PROGRA~~1/R/R-35~~1.0/etc/i386/Makeconf:215: eliasFano.o] Error 1
ERROR: compilation failed for package 'scfind'

removing 'C:/Program Files/R/R-3.5.0/library/scfind'
In R CMD INSTALL
Error in i.p(...) :
(converted from warning) installation of package ‘C:/Users/hashime/AppData/Local/Temp/RtmpoJWtAD/file1eb0a42416e/scfind_3.1.0.tar.gz’ had non-zero exit status

Problem installing scfind

Hello,
I get an error message when trying to install scfind and I need help to figure it out, how to fix it.

version R version 3.6.1 (2019-07-05)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)

devtools::install_github(repo="hemberg-lab/scfind", ref="master")
Downloading GitHub repo hemberg-lab/scfind@master
√ checking for file 'C:\Users\u0125188\AppData\Local\Temp\RtmpG2SLlH\remotes1fcc44932a93\hemberg-lab-scfind-388c394/DESCRIPTION' ...

preparing 'scfind':
√ checking DESCRIPTION meta-information ...
cleaning src
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories
looking to see if a 'data/datalist' file should be added
building 'scfind_3.5.0.tar.gz'

Installing package into ‘C:/Users/u0125188/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

installing source package 'scfind' ...
** using staged installation
** libs

*** arch - i386
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c eliasFano.cpp -o eliasFano.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c fp_growth.cpp -o fp_growth.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c functions.cpp -o functions.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c serialization.cpp -o serialization.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scfind.dll tmp.def RcppExports.o eliasFano.o fp_growth.o functions.o serialization.o -LC:/Users/u0125188/DOCUME1/R/R-3.6.1/bin/i386 -lR
installing to C:/Users/u0125188/Documents/R/win-library/3.6/00LOCK-scfind/00new/scfind/libs/i386

*** arch - x64
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c eliasFano.cpp -o eliasFano.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c fp_growth.cpp -o fp_growth.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c functions.cpp -o functions.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/u0125188/DOCUME1/R/R-3.6.1/include" -DNDEBUG -I"C:/Users/u0125188/Documents/R/win-library/3.6/Rcpp/include" -I"C:/Users/u0125188/Documents/R/win-library/3.6/RcppArmadillo/include" -O2 -Wall -mtune=generic -c serialization.cpp -o serialization.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scfind.dll tmp.def RcppExports.o eliasFano.o fp_growth.o functions.o serialization.o -LC:/Users/u0125188/DOCUME1/R/R-3.6.1/bin/x64 -lR
installing to C:/Users/u0125188/Documents/R/win-library/3.6/00LOCK-scfind/00new/scfind/libs/x64
** R
Error : (converted from warning) unable to re-encode 'CoreMethods.R' lines 421, 422, 423, 424, 449, 461, 466, 481, 494, 503
ERROR: unable to collate and parse R files for package 'scfind'

removing 'C:/Users/u0125188/Documents/R/win-library/3.6/scfind'
Error: Failed to install 'scfind' from GitHub:
(converted from warning) installation of package ‘C:/Users/u0125188/AppData/Local/Temp/RtmpG2SLlH/file1fcc37eb970/scfind_3.5.0.tar.gz’ had non-zero exit status

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