ERROR: compilation failed for package 'presto'

[SeadonXing]

Hi ! Thank you for creating such cool software.

I got some trouble when I installed the presto.

I first try these commands:

library(devtools)
 install_github('immunogenomics/presto')

Then I got the following errors:

Downloading GitHub repo immunogenomics/presto@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  can't open URL'https://api.github.com/repos/immunogenomics/presto/tarball/HEAD'

So I downloaded the source code of presto from GitHub, and install it from the local with these commands : devtools::install_local("D:/Software/Presto/presto-master.zip")

Then I got the following errors:

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

*** arch - i386
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/Program Files/R/R-4.1.0/include" -DNDEBUG  -I'D:/Program Files/R/R-4.1.0/library/Rcpp/include' -I'D:/Program Files/R/R-4.1.0/library/RcppArmadillo/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"D:/Program Files/R/R-4.1.0/include" -DNDEBUG  -I'D:/Program Files/R/R-4.1.0/library/Rcpp/include' -I'D:/Program Files/R/R-4.1.0/library/RcppArmadillo/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fast_wilcox.cpp -o fast_wilcox.o
fast_wilcox.cpp: In function 'std::__cxx11::list<float> cpp_in_place_rank_mean(arma::vec&, int, int)':
fast_wilcox.cpp:116:34: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
     for (size_t i = idx_begin; i <= idx_end; i++) {
                                ~~^~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o presto.dll tmp.def RcppExports.o fast_wilcox.o -LD:/Program Files/R/R-4.1.0/bin/i386 -lR
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/libstdc++.a(c++locale.o):(.text$_ZSt14__convert_to_vIfEvPKcRT_RSt12_Ios_IostateRKPi+0x6a): undefined reference to `__mingw_strtof'
C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/../../../../i686-w64-mingw32/bin/ld.exe: C:/rtools40/mingw32/bin/../lib/gcc/i686-w64-mingw32/8.3.0/libstdc++.a(c++locale.o):(.text$_ZSt14__convert_to_vIdEvPKcRT_RSt12_Ios_IostateRKPi+0x6a): undefined reference to `__mingw_strtod'
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'presto'
 removing 'D:/Program Files/R/R-4.1.0/library/presto'
Warning message:
In i.p(...) :
  installation of package ‘C:/Users/admin/AppData/Local/Temp/RtmpCKCvXd/remotes428c7f519c8/presto-master’ had non-zero exit status

And I can't install and found presto from CRAN. Could you please help me or share with me the binary version of presto ? Thank you in advance for your help. And I hope I can install presto from CRAN or Bioconductor soon ^*^.

Best wishes!

[slowkow]

Thanks for reporting the issue.

The important error in your messages is this:

undefined reference to `__mingw_strtof'

Searching for "undefined reference to `__mingw_strtof'" takes me to this report:

• https://gcc.gnu.org/bugzilla/show_bug.cgi?id=57220

The last comment on that page says:

I couldn't resist and removed all gcc entries from the env PATH, which solved the problem. I apologize for the unnecessary trouble I have caused - at least I learned several new things about mingw.

In other words, you might consider trying to reconfigure your system, and then compilation might work. Sorry for the hassle.

[SeadonXing]

Dear Kamil,

Thank you very much for your help ! I reinstalled Rtools and installed presto from the local, which solved the problem.

Now I am enjoying the presto ! Many thanks ! Seadon

[massonix]

Hi presto team, thanks for developing this tool!

I obtain a similar error:

> remotes::install_github('immunogenomics/presto')
Downloading GitHub repo immunogenomics/presto@HEAD
Error: Failed to install 'presto' from GitHub:
  Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

Any idea what could be the issue?

[slowkow]

@massonix Could you try running pkgbuild::check_build_tools(debug = TRUE) and reporting the output?

[Byronxy]

I met the same issue in Ubuntu 20. I figure it our by installing in R console rather than in Rstudio

[denvercal1234GitHub]

pkgbuild::check_build_tools(debug = TRUE) Your system is ready to build packages!

Hi @slowkow, I still obtained error while aiming to install the package which is a dependency to the Azimuth package I needed. Any advice to address this error? Thank you so much!

> install_github('immunogenomics/presto')
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo immunogenomics/presto@HEAD
✔  checking for file ‘/private/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T/RtmptApd9r/remotes9058745962de/immunogenomics-presto-052085d/DESCRIPTION’ ...
─  preparing ‘presto’:
✔  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 ‘presto_1.0.0.tar.gz’

* installing *source* package ‘presto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:26: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:642:60: error: no template named 'numeric_limits'
    bool _FloatBigger = (numeric_limits<_FloatT>::digits > numeric_limits<_IntT>::digits),
                                                           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:18: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:643:50: error: no template named 'numeric_limits'
    int _Bits = (numeric_limits<_IntT>::digits - numeric_limits<_FloatT>::digits)>
                                                 ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:648:17: error: no template named 'numeric_limits'
  static_assert(numeric_limits<_FloatT>::radix == 2, "FloatT has incorrect radix");
                ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:25: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() :  (numeric_limits<_IntT>::max() >> _Bits << _Bits);
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:651:58: error: no template named 'numeric_limits'
  return _FloatBigger ? numeric_limits<_IntT>::max() :  (numeric_limits<_IntT>::max() >> _Bits << _Bits);
                                                         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:645:25: error: no return statement in constexpr function
_LIBCPP_CONSTEXPR _IntT __max_representable_int_for_float() _NOEXCEPT {
                        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:661:16: error: no template named 'numeric_limits'
  using _Lim = numeric_limits<_IntT>;
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:664:12: error: use of undeclared identifier '_Lim'
    return _Lim::max();
           ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:665:21: error: use of undeclared identifier '_Lim'
  } else if (__r <= _Lim::lowest()) {
                    ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:666:12: error: use of undeclared identifier '_Lim'
    return _Lim::min();
           ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:153:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:437:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__hash_table:16:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:490:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__algorithm/search.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__iterator/incrementable_traits.h:14:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/concepts:134:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:22:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:83:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdlib:138:9: error: target of using declaration conflicts with declaration already in scope
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
/usr/local/include/stdlib.h:132:6: note: target of using declaration
int      abs(int) __pure2;
         ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: conflicting declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:853:1: error: declaration conflicts with target of using declaration already in scope
abs(const complex<_Tp>& __c)
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: target of using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:9: note: using declaration
using ::abs _LIBCPP_USING_IF_EXISTS;
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:910:16: error: reference to unresolved using declaration
        return abs(__c.real());
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:912:16: error: reference to unresolved using declaration
        return abs(__c.imag());
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:969:16: error: reference to unresolved using declaration
        __re = abs(__re);
               ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1022:29: error: reference to unresolved using declaration
    return complex<_Tp>(log(abs(__x)), arg(__x));
                            ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include/RcppCommon.h:65:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/complex:1049:23: error: reference to unresolved using declaration
    return polar(sqrt(abs(__x)), arg(__x) / _Tp(2));
                      ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
using ::abs _LIBCPP_USING_IF_EXISTS;
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘presto’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/presto’
Warning in i.p(...) :
  installation of package ‘/var/folders/yf/mfkcsd412qndhd65fdwcz7l40000gn/T//RtmptApd9r/file9058186a187f/presto_1.0.0.tar.gz’ had non-zero exit status