msa.install

[Yikun]

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL msa
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘msa’ ...
** using staged installation
** libs

make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalW
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/ClustalW'
./configure; \
cd src; \
export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result"; \
/home/biocbuild/bbs-3.17-bioc/R/bin/R CMD SHLIB -o libClustalW.so pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp && \
ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \
cp libClustalW.a ../../
checking build system type... ./config.guess: unable to guess system type

This script, last modified 2009-06-10, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from

  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
and
  http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD

If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <config-patches@gnu.org> in order to provide the needed
information to handle your system.

config.guess timestamp = 2009-06-10

uname -m = aarch64
uname -r = 5.15.0-58-generic
uname -s = Linux
uname -v = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023

/usr/bin/uname -p = aarch64
/bin/uname -X     =

hostinfo               =
/bin/universe          =
/usr/bin/arch -k       =
/bin/arch              = aarch64
/usr/bin/oslevel       =
/usr/convex/getsysinfo =

UNAME_MACHINE = aarch64
UNAME_RELEASE = 5.15.0-58-generic
UNAME_SYSTEM  = Linux
UNAME_VERSION = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023
configure: error: cannot guess build type; you must specify one
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/ClustalW/src'
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include   -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result -fPIC  -g -O2  -Wall  -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
pairwise/FullPairwiseAlign.cpp:7:14: fatal error: config.h: No such file or directory
    7 |     #include "config.h"
      |              ^~~~~~~~~~
compilation terminated.
make[2]: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: pairwise/FullPairwiseAlign.o] Error 1
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/ClustalW/src'
make[1]: *** [msaMakefile:8: clustalw] Error 1
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/msa/src/ClustalW'
make: *** [Makevars:28: build_clustalw] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/msa’

[Yikun]

https://github.com/UBod/msa/issues/23

https://github.com/UBod/msa/pull/24

[martin-g]

msa still fails but for a different reason. Same failure on x86_64 - https://bioconductor.org/checkResults/3.17/bioc-LATEST/msa/nebbiolo1-buildsrc.html

[martin-g]

https://bioconductor.org/checkResults/3.18/bioc-LATEST/msa/kunpeng2-buildsrc.html build fine! There are warnings in check