I am trying to install blasr on mac osx.
I followed the steps here
I get the error below after using the 'make' command:
make PREFIX=/tmp/pitchfork blasr
Cloning into 'pitchfork'...
remote: Counting objects: 10203, done.
remote: Compressing objects: 100% (51/51), done.
remote: Total 10203 (delta 25), reused 51 (delta 18), pack-reused 10128
Receiving objects: 100% (10203/10203), 1.16 MiB | 207.00 KiB/s, done.
Resolving deltas: 100% (5413/5413), done.
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f mk/init.mk init
/Users/cr517/Documents/pitchfork/bin/checkSystem
/Users/cr517/Documents/pitchfork/bin/checkCC gcc
mkdir -p "/Users/cr517/Documents/pitchfork/workspace"
mkdir -p "/Users/cr517/Documents/pitchfork/distfiles"
mkdir -p "/Users/cr517/Documents/pitchfork/staging"
mkdir -p "/tmp/pitchfork/bin"
mkdir -p "/tmp/pitchfork/etc"
mkdir -p "/tmp/pitchfork/include"
mkdir -p "/tmp/pitchfork/lib"
mkdir -p "/tmp/pitchfork/lib/pkgconfig"
mkdir -p "/tmp/pitchfork/share"
mkdir -p "/tmp/pitchfork/var/pkg"
echo "export DYLD_LIBRARY_PATH=/tmp/pitchfork/lib:\$DYLD_LIBRARY_PATH"|sed -e 's/::*/:/g' > "/tmp/pitchfork/setup-env.sh"
echo "export PATH=/tmp/pitchfork/bin:\$PATH"|sed -e 's/::*/:/g' >> "/tmp/pitchfork/setup-env.sh"
echo "OLDPS1=\$PS1" >> "/tmp/pitchfork/setup-env.sh"
echo "[[ \"\$PS1\" ]] && PS1=\"pitchfork($(/Users/cr517/Documents/pitchfork/bin/pitchfork short-branch)) \$PS1\" || PS1=\($(/Users/cr517/Documents/pitchfork/bin/pitchfork short-branch)\)" >> "/tmp/pitchfork/setup-env.sh"
touch mk//../initialized.o
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/zlib do-install
make[1]: Nothing to be done for `do-install'.
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/libbzip2 do-install
rm -rf /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6
mkdir -p /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/pkgconfig /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/include /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/bin
cp -aL /usr/bin/bzip2 /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/bin/
cp -aL /usr/include/bzlib.h /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/include
cp -aL /usr/lib/libbz2.* /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib
ln -sfn libbz2.dylib.1.0 /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/libbz2.dylib.1
ln -sfn libbz2.dylib.1 /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/libbz2.dylib
sed -e "s@^prefix=.*@prefix=/tmp/pitchfork@" bzip2.pc > /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/pkgconfig/bzip2.pc
cd /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6 && tar cf - * | tar xf - -C /tmp/pitchfork
find /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6 ! -type d|awk -F '/Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/' '{print $2}' > /tmp/pitchfork/var/pkg/libbzip2-1.0.6
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/boost do-install
/Users/cr517/Documents/pitchfork/bin/pitchfork fetch --url https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
fetching https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
{'url': 'https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz', 'subcommand': 'fetch'}
Traceback (most recent call last):
File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 525, in <module>
sys.exit(main())
File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 518, in main
pitchfork(pargs)
File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 444, in pitchfork
raise Exception("[ERROR] %s" % ''.join(_err))
Exception: [ERROR] --2018-01-24 00:35:30-- https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
Resolving prdownloads.sourceforge.net... 216.34.181.59
Connecting to prdownloads.sourceforge.net|216.34.181.59|:443... connected.
ERROR: cannot verify prdownloads.sourceforge.net's certificate, issued by ‘CN=COMODO RSA Domain Validation Secure Server CA,O=COMODO CA Limited,L=Salford,ST=Greater Manchester,C=GB’:
Unable to locally verify the issuer's authority.
To connect to prdownloads.sourceforge.net insecurely, use `--no-check-certificate'.
make[1]: *** [boost_1_60_0.tar.gz] Error 1
make: *** [boost] Error 2
I think the important info is here:
raise Exception("[ERROR] %s" % ''.join(_err))
Exception: [ERROR] --2018-01-24 00:35:30-- https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
Resolving prdownloads.sourceforge.net... 216.34.181.59
Connecting to prdownloads.sourceforge.net|216.34.181.59|:443... connected.
ERROR: cannot verify prdownloads.sourceforge.net's certificate, issued by ‘CN=COMODO RSA Domain Validation Secure Server CA,O=COMODO CA Limited,L=Salford,ST=Greater Manchester,C=GB’:
Unable to locally verify the issuer's authority.
To connect to prdownloads.sourceforge.net insecurely, use `--no-check-certificate'.
but how can I specify the --no-check-certificate option? That's not a make option, I've tried it.
I tried homebrew but got this message:
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 2 taps (caskroom/cask, caskroom/versions).
Warning: Calling 'depends_on :mysql' is deprecated!
Use 'depends_on "mysql"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blat.rb:19:in `<class:Blat>'
Please report this to the brewsci/science tap!
Warning: Calling 'depends_on :python3' is deprecated!
Use 'depends_on "python3"' instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/matplotlib.rb:56:in `<class:Matplotlib>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
==> Installing blasr from brewsci/science
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
Warning: Calling <<-EOS.undent is deprecated!
Use <<~EOS instead.
/usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
Please report this to the brewsci/science tap!
==> Downloading https://github.com/PacificBiosciences/blasr/archive/smrtanalysis
Already downloaded: /Users/cr517/Library/Caches/Homebrew/blasr-2.2.tar.gz
==> make STATIC= HDF5INCLUDEDIR=/usr/local/opt/hdf5/include HDF5LIBDIR=/usr/loca
Last 15 lines from /Users/cr517/Library/Logs/Homebrew/blasr/01.make:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4912:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const RegionAnnotation'
operator<(const shared_ptr<_Tp>& __x, const shared_ptr<_Up>& __y) _NOEXCEPT
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4977:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const RegionAnnotation'
operator<(const shared_ptr<_Tp>& __x, nullptr_t) _NOEXCEPT
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4985:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const int'
operator<(nullptr_t, const shared_ptr<_Tp>& __x) _NOEXCEPT
^
1 error generated.
make[1]: *** [bin/KBandMatcher.o] Error 1
make: *** [alignment-build] Error 2
make: *** [sequtils-build] Error 2
clang++ -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include bin/PrintPBBWT.o -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -lz -lpthread
clang++ -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include bin/BWTQuery.o -o bin/bwtquery -L/usr/local/opt/hdf5/lib -lz -lpthread
If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/brewsci/homebrew-science/issues
I still need to report the issue at the provided address.
I tried Anaconda 'conda install -c bioconda blasr ':
PackageNotFoundError: Packages missing in current channels:
- blasr
We have searched for the packages in the following channels:
- https://conda.anaconda.org/bioconda/osx-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/osx-64
- https://conda.anaconda.org/conda-forge/noarch
- https://conda.anaconda.org/r/osx-64
- https://conda.anaconda.org/r/noarch
- https://repo.continuum.io/pkgs/main/osx-64
- https://repo.continuum.io/pkgs/main/noarch
- https://repo.continuum.io/pkgs/free/osx-64
- https://repo.continuum.io/pkgs/free/noarch
- https://repo.continuum.io/pkgs/r/osx-64
- https://repo.continuum.io/pkgs/r/noarch
- https://repo.continuum.io/pkgs/pro/osx-64
- https://repo.continuum.io/pkgs/pro/noarch
conda install -c bioconda blasr
, okay in June 2022 on z shell of macos $\endgroup$