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Cannot install sra-tools #954

Closed bentyeh closed 1 month ago

bentyeh commented 3 months ago

I followed the instructions in the Wiki to build (compile) and install the SRA Toolkit, but the install process failed with the following error message (last 13 lines of stderr shown):

...
CMAKE_VERSION=3.20.2
BUILD_TOOLS_INTERNAL=OFF
BUILD_TOOLS_LOADERS=OFF
BUILD_TOOLS_TEST_TOOLS=OFF
TOOLS_ONLY=ON
VERSION=3.1.1
LIBXML2_INCLUDE_DIR=/usr/include/libxml2
LIBXML2_LIBRARIES=/usr/lib64/libxml2.so
Using ncbi-vdb interfaces: /central/scratch/btyeh/sra_src/ncbi-vdb/interfaces
Using ncbi-vdb binary libraries: /central/scratch/btyeh/sra_build/ncbi-vdb/linux/gcc/x86_64/rel/lib
RUN_SANITIZER_TESTS: 
mkdir: cannot create directory ‘/central/scratch/btyeh/sra_src/sra-tools/shared/kfgsums’: File exists
cp: failed to access '/central/scratch/btyeh/sra_src/sra-tools/shared/kfgsums/vdb-copy.kfg': Not a directory

The script I used to try to build and install the toolkit is as follows:

cd ~/tmp

DIR_WD="$(pwd -P)"

# create directories
mkdir sra_install
mkdir sra_build
mkdir sra_src

# download source code
cd sra_src
git clone https://github.com/ncbi/ncbi-vdb.git
git clone https://github.com/ncbi/sra-tools.git

# build ncbi-vdb
cd ncbi-vdb
./configure --build-prefix="$DIR_WD/sra_build" --prefix="$DIR_WD/sra_install"
make
make install

# build sra-tools
cd ../sra-tools
./configure --build-prefix="$DIR_WD/sra_build" --prefix="$DIR_WD/sra_install"
make
make install

I can confirm that the error is occurring during the final make install command.

Any help is appreciated!

bentyeh commented 3 months ago

I tried using cmake (following https://github.com/ncbi/sra-tools/issues/937#issuecomment-2129704817) with the same result.

mkdir -p tmp && cd tmp
DIR_TMP="$(pwd -P)"
mkdir sratoolkit
git clone https://github.com/ncbi/ncbi-vdb.git
git clone https://github.com/ncbi/sra-tools.git
mkdir build
cd build
cmake -S "$DIR_TMP/ncbi-vdb" -B ncbi-vdb
cmake --build ncbi-vdb
cmake -D VDB_LIBDIR="$(pwd -P)/ncbi-vdb/lib" -D CMAKE_INSTALL_PREFIX="$DIR_TMP/sratoolkit" -S "$DIR_TMP/sra-tools" -B sra-tools 
cmake --build sra-tools --target install
bentyeh commented 3 months ago

I also tried using the 3.1.1 releases of both ncbi-vdb and sra-tools instead of using the latest commits in the git repositories, with the same error:

mkdir -p tmp && cd tmp
DIR_TMP="$(pwd -P)"
mkdir sratoolkit

wget -O ncbi-vdb.tar.gz https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.1.1.tar.gz
tar -xzf ncbi-vdb.tar.gz
mv ncbi-vdb-3.1.1 ncbi-vdb

wget -O sra-tools.tar.gz https://github.com/ncbi/sra-tools/archive/refs/tags/3.1.1.tar.gz
tar -xzf sra-tools.tar.gz
mv sra-tools-3.1.1 sra-tools

mkdir build
cd build
cmake -S "$DIR_TMP/ncbi-vdb" -B ncbi-vdb
cmake --build ncbi-vdb
cmake -D VDB_LIBDIR="$(pwd -P)/ncbi-vdb/lib" -D CMAKE_INSTALL_PREFIX="$DIR_TMP/sratoolkit" -S "$DIR_TMP/sra-tools" -B sra-tools 
cmake --build sra-tools --target install

Environment

klymenko commented 3 months ago

The output does not match the script.

Run the commands from the script one-by-one from command line.

bentyeh commented 3 months ago

Hi Andrew, I separately capture standard output and standard error. The output above is only from standard error. Do you mean that you want to see the standard output as well?

klymenko commented 3 months ago

Yes, everything together.

bentyeh commented 3 months ago

Here's the tail of the output. You can see the error in lines 11-12 of what I share below. But it seems like the installation continues past the error, so does that mean that the build/installation still finished correctly and successfully?

...

[ 99%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o
[ 99%] Linking CXX executable ../../../bin/sratools
[ 99%] Built target sratools
[ 99%] Building CXX object tools/external/sra-info/CMakeFiles/sra-info.dir/main.cpp.o
[ 99%] Building CXX object tools/external/sra-info/CMakeFiles/sra-info.dir/sra-info.cpp.o
[ 99%] Building CXX object tools/external/sra-info/CMakeFiles/sra-info.dir/formatter.cpp.o
[100%] Linking CXX executable ../../../bin/sra-info
[100%] Built target sra-info
Install the project...
-- Install configuration: "Debug"
mkdir: cannot create directory ‘/central/scratch/btyeh/sra_cmake_release/sra-tools/shared/kfgsums’: File exists
cp: failed to access '/central/scratch/btyeh/sra_cmake_release/sra-tools/shared/kfgsums/vdb-copy.kfg': Not a directory
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs-c++.a.3.1.1
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs-c++.a.3
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs-c++.a
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs-c++-static.a
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ncbi-vdb/NGS.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/FragTest.cpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/AlignTest.cpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/AlignSliceTest.cpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/PileupTest.cpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/RefTest.cpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/DumpReferenceFASTA.cpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/expected.txt
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/Makefile
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples/README.txt
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libngs-c++.a.3.1.1
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libngs-c++.a.3
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libngs-c++.a
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libngs-c++-static.a
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libngs-c++.so.3.1.1
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libngs-c++.so.3
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libngs-c++.so
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs.a.3.1.1
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs.a.3
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs.a
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs-static.a
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs.so.3.1.1
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs.so.3
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/lib64/libncbi-ngs.so
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/AlignmentIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/Fragment.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/ReferenceSequence.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/StringRef.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/ReadGroup.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/Package.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/Refcount.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/StringItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/ReadItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/PileupItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/PileupEventItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/ReadCollectionItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/ErrorMsg.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/ReadGroupItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/FragmentItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/StatisticsItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/AlignmentItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/ReferenceSequenceItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/ReferenceItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/adapter/defs.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/PileupEventIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/ReferenceIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/Alignment.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/win
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/win/stdbool.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/win/atomic32.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/PileupEvent.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/PileupIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/ReadIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/AlignmentIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/Fragment.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/ReferenceSequence.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/StringRef.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/ReadGroup.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/Package.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/PileupEventIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/ReferenceIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/Alignment.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/PileupEvent.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/PileupIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/ReadIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/Statistics.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/ReadGroupIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/ReadCollection.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/Pileup.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/FragmentIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/Read.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/inl/Reference.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/ErrorMsg.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/Statistics.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/ReadGroupIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/ReadCollection.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReferenceItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/Refcount.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/StringItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReadItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/PileupItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ErrBlock.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/PackageItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReadCollectionItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReferenceSequenceItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/VTable.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/StatisticsItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/PileupEventItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/Refcount.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/PileupEventItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/AlignmentItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReadItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReadCollectionItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ErrorMsg.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReadGroupItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/FragmentItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReadGroupItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/FragmentItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/StringItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/StatisticsItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/PileupItf.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/AlignmentItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReferenceSequenceItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ErrBlock.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/ReferenceItf.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/VTable.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/itf/defs.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/Pileup.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix/x86_64
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix/x86_64/atomic32.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix/fat86
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix/fat86/atomic32.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix/arm64
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix/arm64/atomic32.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix/i386
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/unix/i386/atomic32.h
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/FragmentIterator.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/Read.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/include/ngs/Reference.hpp
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/jar/ngs-java.jar
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/examples/AlignTest.java
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/examples/AlignSliceTest.java
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/examples/FragTest.java
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/examples/PileupTest.java
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/examples/RefTest.java
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/examples/ReadGroupTest.java
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/examples/DumpReferenceFASTA.java
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/Makefile
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/README.txt
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/examples-java/expected.txt
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/jar/ngs-examples.jar
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/index.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/stylesheet.css
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/help-doc.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov/nih
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov/nih/nlm
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov/nih/nlm/ncbi
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/allclasses.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/overview-summary.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/index-all.html
-- Installing: /central/scratch/btyeh/sra_cmake_release/sra_install/share/javadoc/ngs-doc/deprecated-list.html
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klymenko commented 3 months ago

The output does not match the script. I need to see the output of configure. Run the commands from the script one-by-one from command line.

What is the value of $DIR_WD ?

bentyeh commented 3 months ago

I apologize for the confusing directories, as I have been testing across different devices.

Here's an attempt on GitHub Codespaces.

#!/bin/bash

DIR_TMP='/home/codespace/tmp'
mkdir -p "$DIR_TMP"
cd "$DIR_TMP"

# create directories
mkdir install
mkdir build
mkdir src

# download source code
cd "$DIR_TMP/src"

wget -O sra-tools.tar.gz https://github.com/ncbi/sra-tools/archive/refs/tags/3.1.1.tar.gz
tar -xzf sra-tools.tar.gz
mv sra-tools-3.1.1 sra-tools
rm sra-tools.tar.gz

wget -O ncbi-vdb.tar.gz https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.1.1.tar.gz
tar -xzf ncbi-vdb.tar.gz
mv ncbi-vdb-3.1.1 ncbi-vdb
rm ncbi-vdb.tar.gz

# build ncbi-vdb
cd "$DIR_TMP/src/ncbi-vdb"
./configure --build-prefix="$DIR_TMP/build" --prefix="$DIR_TMP/install" &> "$DIR_TMP/log_vdb_configure.log"
make &> "$DIR_TMP/log_vdb_make.log"
make install &> "$DIR_TMP/log_vdb_make_install.log"

# build sra-tools
cd "$DIR_TMP/src/sra-tools"
./configure --build-prefix="$DIR_TMP/build" --prefix="$DIR_TMP/install" &> "$DIR_TMP/log_sra_configure.log"
make &> "$DIR_TMP/log_sra_make.log"
make install &> "$DIR_TMP/log_sra_make_install.log"

Here are the individual log files

klymenko commented 3 months ago

@bentyeh, thank you for your report.

install process failed

Install process fails when its return code is not 0.

mkdir: cannot create directory ‘..._src/sra-tools/shared/kfgsums’: File exists cp: failed to access '..._src/sra-tools/shared/kfgsums/vdb-copy.kfg': Not a directory

Please ignore those messages. Thank you for finding them, we are going to fix this bug.

the error is occurring during the final make install command

Please ignore this error, make install is successful.

installation continues past the error, so does that mean that the build/installation still finished correctly and successfully?

Correct.