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hjshayya254
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@hjshayya254-17788
Last seen 6.1 years ago
I'm encountering an issue trying to install flipflop on our Linux server. I've tried to do this the typical way, simply typing the following into RStudio:
source("https://bioconductor.org/biocLite.R")
biocLite("flipflop")
The package seems to download properly and begin compiling. However, there seems to be an error compiling align.cpp, as I receive the following output:
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) ‘flipflop’
trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/flipflop_1.18.0.tar.gz'
Content type 'application/x-gzip' length 453566 bytes (442 KB)
==================================================
downloaded 442 KB
* installing *source* package ‘flipflop’ ...
** libs
g++ -I"/usr/share/R/include" -DNDEBUG -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oNcpyf/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c FileSplitter.cpp -o FileSplitter.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oNcpyf/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_flipflop.c -o R_init_flipflop.o
g++ -I"/usr/share/R/include" -DNDEBUG -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -fopenmp -DUSE_BLAS_LIB -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-oNcpyf/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c align.cpp -o align.o
In file included from align.h:5:0,
from align.cpp:5:
commontype.h: In function ‘range_t make_range_t(long int, long int)’:
commontype.h:18:75: error: no matching function for call to ‘make_pair<long int, long int>(long int&, long int&)’
inline range_t make_range_t(long a,long b){return make_pair<long,long>(a,b);}
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/ios:40,
from /usr/include/c++/7/ostream:38,
from /usr/include/c++/7/iostream:39,
from align.cpp:1:
/usr/include/c++/7/bits/stl_pair.h:519:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
make_pair(_T1&& __x, _T2&& __y)
^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:519:5: note: template argument deduction/substitution failed:
In file included from align.h:5:0,
from align.cpp:5:
commontype.h:18:75: note: cannot convert ‘a’ (type ‘long int’) to type ‘long int&&’
inline range_t make_range_t(long a,long b){return make_pair<long,long>(a,b);}
^
/usr/lib/R/etc/Makeconf:168: recipe for target 'align.o' failed
make: *** [align.o] Error 1
ERROR: compilation failed for package ‘flipflop’
* removing ‘/home/hani/R/x86_64-pc-linux-gnu-library/3.5/flipflop’
As far as I can tell this doesn't seem to be a general problem with our server: I am able to successfully install other R/bioconductor packages and I encountered the same issue when trying to install flipflop on a different server we have in lab.
I'm wondering if there is something I should be doing differently for the installation or perhaps some dependencies I missed installing? I've provided my sessionInfo below and am extremely grateful for any help you may be able to provide!
> sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.30.0 loaded via a namespace (and not attached): [1] compiler_3.5.1 tools_3.5.1 yaml_2.2.0
I think I've fixed the problem and am providing an update here in case it helps others.
As far as I can tell it was a problem with the C++ standard that GCC was using to compile the source. I don't know anything about C++, but as far as I can tell from googling there have been some changes to the make_pair function, which may explain the error that was being thrown above. Anyways, I find that passing the flag -std=c++98 to GCC seems to allow proper compilation of align.cpp and everything else.
To get flipflop installed what I ended up doing was downloaded the .tar.gz archive from bioconductor, unzipping and manually adding the line CXX_STD = CXX98 to the Makevars file in the src subdirectory.
I then re-zipped and installed the package directly in R:
I am sure this is a horrifically inefficient way of doing things and would welcome input from others with more knowledge of this particular issue. Perhaps there is an elegant solution (install.packages has a 'configure.vars' option that perhaps could be used to set the CXXFLAGS environment variable? I have not tested)? Anyways, it seemed to work for me...
Thanks for working this out! I was having the same problem. I know Elsa so I'll ping her about this. Edit: maybe you could set your ~/.R/Makevars to use C++98? I don't know if bioconductor respects that or not though.