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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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compilation error on OpenSuse tumbleweed #284

Closed SinomeM closed 1 year ago

SinomeM commented 1 year ago

Hi I'm getting the following error while trying to install the package:

> BiocManager::install('mzR')
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for
details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Installing package(s) 'mzR'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/mzR_2.34.0.tar.gz'
Content type 'application/x-gzip' length 7656299 bytes (7.3 MB)
==================================================
downloaded 7.3 MB

* installing *source* package ‘mzR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++-12 (SUSE Linux) 12.3.0’
using C++11
rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o
g++ -std=gnu++11 -I"/usr/lib64/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/home/simone/R/x86_64-suse-linux-gnu-library/4.3/Rcpp/include' -I'/home/simone/R/x86_64-suse-linux-gnu-library/4.3/Rhdf5lib/include' -I/usr/local/include    -fpic  -O2 -Wall -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=3 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -flto=auto -g  -c RcppPwiz.cpp -o RcppPwiz.o
In file included from pwiz/data/msdata/MSDataFile.hpp:29,
                 from RcppPwiz.h:12,
                 from RcppPwiz.cpp:1:
pwiz/data/msdata/MSData.hpp:425:18: error: ‘int64_t’ in namespace ‘std’ does not name a type
  425 |     typedef std::int64_t value_type;
      |                  ^~~~~~~
pwiz/data/msdata/MSData.hpp:431:28: error: ‘value_type’ was not declared in this scope
  431 |     pwiz::util::BinaryData<value_type> data;
      |                            ^~~~~~~~~~
pwiz/data/msdata/MSData.hpp:431:38: error: template argument 1 is invalid
  431 |     pwiz::util::BinaryData<value_type> data;
      |                                      ^
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from pwiz/data/msdata/MSDataFile.hpp:31:
pwiz/data/msdata/BinaryDataEncoder.hpp: At global scope:
pwiz/data/msdata/BinaryDataEncoder.hpp:87:40: error: ‘int64_t’ is not a member of ‘std’
   87 |     void encode(const std::vector<std::int64_t>& data, std::string& result, size_t* binaryByteCount = NULL) const;
      |                                        ^~~~~~~
pwiz/data/msdata/BinaryDataEncoder.hpp:87:40: note: suggested alternatives:
In file included from /usr/include/sys/types.h:155,
                 from /usr/include/stdlib.h:395,
                 from /usr/include/c++/13/bits/std_abs.h:38,
                 from /usr/include/c++/13/cmath:49,
                 from /home/simone/R/x86_64-suse-linux-gnu-library/4.3/Rcpp/include/Rcpp/platform/compiler.h:100,
                 from /home/simone/R/x86_64-suse-linux-gnu-library/4.3/Rcpp/include/Rcpp/r/headers.h:62,
                 from /home/simone/R/x86_64-suse-linux-gnu-library/4.3/Rcpp/include/RcppCommon.h:30,
                 from /home/simone/R/x86_64-suse-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4:
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
   27 | typedef __int64_t int64_t;
      |                   ^~~~~~~
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
pwiz/data/msdata/BinaryDataEncoder.hpp:87:40: error: ‘int64_t’ is not a member of ‘std’
   87 |     void encode(const std::vector<std::int64_t>& data, std::string& result, size_t* binaryByteCount = NULL) const;
      |                                        ^~~~~~~
pwiz/data/msdata/BinaryDataEncoder.hpp:87:40: note: suggested alternatives:
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
   27 | typedef __int64_t int64_t;
      |                   ^~~~~~~
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
pwiz/data/msdata/BinaryDataEncoder.hpp:87:47: error: template argument 1 is invalid
   87 |     void encode(const std::vector<std::int64_t>& data, std::string& result, size_t* binaryByteCount = NULL) const;
      |                                               ^
pwiz/data/msdata/BinaryDataEncoder.hpp:87:47: error: template argument 2 is invalid
pwiz/data/msdata/BinaryDataEncoder.hpp:91:28: error: ‘int64_t’ in namespace ‘std’ does not name a type
   91 |     void encode(const std::int64_t* data, size_t dataSize, std::string& result, size_t* binaryByteCount = NULL) const;
      |                            ^~~~~~~
pwiz/data/msdata/BinaryDataEncoder.hpp:100:82: error: ‘int64_t’ is not a member of ‘std’
  100 |     void decode(const char *encodedData, size_t len, pwiz::util::BinaryData<std::int64_t>& result) const;
      |                                                                                  ^~~~~~~
pwiz/data/msdata/BinaryDataEncoder.hpp:100:82: note: suggested alternatives:
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
   27 | typedef __int64_t int64_t;
      |                   ^~~~~~~
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
pwiz/data/msdata/BinaryDataEncoder.hpp:100:82: error: ‘int64_t’ is not a member of ‘std’
  100 |     void decode(const char *encodedData, size_t len, pwiz::util::BinaryData<std::int64_t>& result) const;
      |                                                                                  ^~~~~~~
pwiz/data/msdata/BinaryDataEncoder.hpp:100:82: note: suggested alternatives:
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
   27 | typedef __int64_t int64_t;
      |                   ^~~~~~~
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
pwiz/data/msdata/BinaryDataEncoder.hpp:100:89: error: template argument 1 is invalid
  100 |     void decode(const char *encodedData, size_t len, pwiz::util::BinaryData<std::int64_t>& result) const;
      |                                                                                         ^
pwiz/data/msdata/BinaryDataEncoder.hpp:101:77: error: ‘int64_t’ is not a member of ‘std’
  101 |     void decode(const std::string& encodedData, pwiz::util::BinaryData<std::int64_t>& result) const
      |                                                                             ^~~~~~~
pwiz/data/msdata/BinaryDataEncoder.hpp:101:77: note: suggested alternatives:
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
   27 | typedef __int64_t int64_t;
      |                   ^~~~~~~
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
pwiz/data/msdata/BinaryDataEncoder.hpp:101:77: error: ‘int64_t’ is not a member of ‘std’
  101 |     void decode(const std::string& encodedData, pwiz::util::BinaryData<std::int64_t>& result) const
      |                                                                             ^~~~~~~
pwiz/data/msdata/BinaryDataEncoder.hpp:101:77: note: suggested alternatives:
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
   27 | typedef __int64_t int64_t;
      |                   ^~~~~~~
/usr/include/bits/stdint-intn.h:27:19: note:   ‘int64_t’
pwiz/data/msdata/BinaryDataEncoder.hpp:101:84: error: template argument 1 is invalid
  101 |     void decode(const std::string& encodedData, pwiz::util::BinaryData<std::int64_t>& result) const
      |                                                                                    ^
RcppPwiz.cpp: In member function ‘Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)’:
RcppPwiz.cpp:407:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  407 |       if (current_scan < 1 || current_scan > n_scans) {
      |                               ~~~~~~~~~~~~~^~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)’:
RcppPwiz.cpp:853:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  853 |     } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
      |                                      ~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:863:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::msdata::TimeIntensityPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  863 |       for (int i = 0; i < pairs.size(); i++) {
      |                       ~~^~~~~~~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector<int>, double, double, double)’:
RcppPwiz.cpp:1014:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1014 |       for (int i = 0; i < scanNumbers.size(); i++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:1020:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::msdata::MZIntensityPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1020 |           for (int k=0; k < pairs.size(); k++)
      |                         ~~^~~~~~~~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:200: RcppPwiz.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/home/simone/R/x86_64-suse-linux-gnu-library/4.3/mzR’
Warning in install.packages(...) :
  installation of package ‘mzR’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmp0iZPWg/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib64/R/library
  packages:
    class, KernSmooth, MASS, Matrix, nnet

I undertand that this can be expected and cannot be fixed by me but it requires an update on your side, am I correct?

Thanks, Simone

sneumann commented 1 year ago

Hi, thanks for reporting. Is there a docker container where we can try to reproduce ? So this is on gcc/g++ 12.3.0 ? Seems very similar to https://github.com/sneumann/mzR/issues/285 Yours, Steffen

SinomeM commented 1 year ago

Hi, yes it should be on gcc 12.3. I'll try to replicate the error on the official docker image and be back!

sneumann commented 1 year ago

So maybe doesn't need a Manjaro/OpenSuse container specifically, anything with very recent g++ should trigger it, and the fix would be similar to https://gitlab.kitware.com/vtk/vtk/-/issues/18782 and https://bbs.archlinux.org/viewtopic.php?pid=2100273#p2100273 Yours, Steffen

robert-winkler commented 1 year ago

Hi, on Fedora with GCC Red Hat 13.1.1-2, mzR compiles; I need a running xcms for a 3-days course next week; thus, I will work on Fedora 38 this time. In week 26+, I'm free again to test different compilers/ environments on Manjaro. Could there also be an issue with the boost libraries (a common problem with the trans-proteomic pipeline)?

sneumann commented 1 year ago

So the pwiz code hasn't changed https://github.com/ProteoWizard/pwiz/blob/09bc7650f1b3d4f5f85d018bdb8c6f84b4b1479a/pwiz/data/msdata/BinaryDataEncoder.hpp#L100 so it is not our aged pwiz snapshot we use.

It could be as simple as adding #include <cstdint> somewhere in RcppPwiz.[cpp|h], I can check once I know a container to easily reproduce. Unsure why it works on GCC Red Hat 13.1.1

Yours, Steffen

jorainer commented 1 year ago

Just general question - wouldn't it maybe be easier for linux users to use the Bioc docker image instead of "system R"? Docker should run almost natively on linux and if there are any security concerns, singularity should be the best alternative. We're using that on our cluster (using the converted BioC docker image).

robert-winkler commented 1 year ago

Johannes Rainer Just general question - wouldn't it maybe be easier for linux users to use the Bioc docker image instead of "system R"? Docker should run almost natively on linux and if there are any security concerns, singularity should be the best alternative. We're using that on our cluster (using the converted BioC docker image). I'm using docker to distribute my new programs and courses. However, I'm not sure if it is the best option for programming R workflows.

Robert Winkler - Chat @ Spike [24cix5]

On June 16, 2023 at 7:01 GMT, Johannes Rainer @.***> wrote:

Just general question - wouldn't it maybe be easier for linux users to use the Bioc docker image instead of "system R"? Docker should run almost natively on linux and if there are any security concerns, singularity should be the best alternative. We're using that on our cluster (using the converted BioC docker image).

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

sneumann commented 1 year ago

Hi, a hint from Kurt Hornik led me to investigate versions:

There was already a fix for this issue, it should be in 2.35.1 https://github.com/sneumann/mzR/commit/a9788d43f52f39968456fafef509e8ddda70896b

and seems to be in BioC devel: http://bioconductor.org/packages/devel/bioc/news/mzR/NEWS

but didn't make it into the current release: http://bioconductor.org/packages/release/bioc/news/mzR/NEWS Can you check this fixes your issue ?

Yours, Steffen

sneumann commented 1 year ago

I cherry-picked the commit into current release version, should be in mzR-2.34.1 shortly. Let's keep fingers crossed, yours, Steffen

https://github.com/sneumann/mzR/commits/RELEASE_3_17

robert-winkler commented 1 year ago

Success! /mzR_2.34.1.tar.gz' compiles properly on Manjaro/Arch:

Robert Winkler - Chat @ Spike [24x0rl]

On June 19, 2023 at 11:55 GMT, Steffen Neumann @.***> wrote:

I cherry-picked the commit into current release version, should be in mzR-2.34.1 shortly. Let's keep fingers crossed, yours, Steffen

https://github.com/sneumann/mzR/commits/RELEASE_3_17

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

sneumann commented 1 year ago

Cool, thanks for the feedback ! Yours, Steffen