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cufflinks fails with boost 1.50.0; works with boost 1.49.0 #14385

Closed
tub78 opened this Issue · 5 comments

4 participants

@tub78

System raring to brew. Output log:
https://gist.github.com/3427889

I found these related discussions online:

My solution was to downgrade to the previous version of boost (1.49.0), like this:
brew uninstall boost
brew cleanup -vs boost
pushd $(brew --prefix)
git checkout -f bf4f9aa Library/Formula/boost.rb
popd
brew install -v boost
brew install -v cufflinks

Thx, -S.

@adamv
Owner

Boo on whoever pulled Boost 1.50.

@adamv
Owner

There's a 2.0.2 version: http://cufflinks.cbcb.umd.edu/

@adamv
Owner

V2 is in beta, requires Eigen, and doesn't compile for me out of the box.

@2bits 2bits referenced this issue from a commit in 2bits/homebrew
@2bits 2bits cufflinks 2.0.2
- Upgrade cufflinks to version 2.0.2
- Add a dep on eigen. It won't build without it.
- Make all the deps `:build` for the same reason.
- It still fails with clang, but llvm is okay.
- Add an env var, `EIGEN_CPPFLAGS` to help it find eigen.
- Add to `LDFLAGS` an `-lboost_system-mt` fixes missing symbols
- Run sed on 120 files to fix a boost::FOREACH issue.
- Note in the comments the source of the sed fix.
- Specify `--mandir` even though no man pages at this time.
- Run `make` in parallel.  Run the install as a j1.
- Works well with superenv

Fixes #14385
809c5f0
@2bits 2bits referenced this issue
Closed

cufflinks 2.0.2 #15543

@2bits

Unlike Macports, we like to fix a thang. Give that a try when it lands.

@adamv adamv closed this issue from a commit
@2bits 2bits cufflinks 2.0.2
- Upgrade cufflinks to version 2.0.2
- Add a dep on eigen. It won't build without it.
- Make all the deps `:build` for the same reason.
- It still fails with clang, but llvm is okay.
- Add an env var, `EIGEN_CPPFLAGS` to help it find eigen.
- Add to `LDFLAGS` an `-lboost_system-mt` fixes missing symbols
- Run sed on 120 files to fix a boost::FOREACH issue.
- Note in the comments the source of the sed fix.
- Specify `--mandir` even though no man pages at this time.
- Run `make` in parallel.  Run the install as a j1.
- Works well with superenv

Fixes #14385

Closes #15543.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
2436e05
@adamv adamv closed this in 2436e05
@theirix theirix referenced this issue from a commit
Commit has since been removed from the repository and is no longer available.
@snakeyroc3 snakeyroc3 referenced this issue from a commit in snakeyroc3/homebrew
@2bits 2bits cufflinks 2.0.2
- Upgrade cufflinks to version 2.0.2
- Add a dep on eigen. It won't build without it.
- Make all the deps `:build` for the same reason.
- It still fails with clang, but llvm is okay.
- Add an env var, `EIGEN_CPPFLAGS` to help it find eigen.
- Add to `LDFLAGS` an `-lboost_system-mt` fixes missing symbols
- Run sed on 120 files to fix a boost::FOREACH issue.
- Note in the comments the source of the sed fix.
- Specify `--mandir` even though no man pages at this time.
- Run `make` in parallel.  Run the install as a j1.
- Works well with superenv

Fixes #14385

Closes #15543.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
c9d948e
@sjackman sjackman referenced this issue from a commit in sjackman/homebrew
@2bits 2bits cufflinks 2.0.2
- Upgrade cufflinks to version 2.0.2
- Add a dep on eigen. It won't build without it.
- Make all the deps `:build` for the same reason.
- It still fails with clang, but llvm is okay.
- Add an env var, `EIGEN_CPPFLAGS` to help it find eigen.
- Add to `LDFLAGS` an `-lboost_system-mt` fixes missing symbols
- Run sed on 120 files to fix a boost::FOREACH issue.
- Note in the comments the source of the sed fix.
- Specify `--mandir` even though no man pages at this time.
- Run `make` in parallel.  Run the install as a j1.
- Works well with superenv

Fixes #14385

Closes #15543.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>
c109677
@liweixie

is this problem fixed for cufflinks install via brew
now, my system always show error
Making all in src
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -arch x86_64 -O3 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
./abundances.h:21:10: fatal error: 'Eigen/Dense' file not found
#include
^
1 error generated.
make[2]: *** [clustering.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

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