Entering edit mode
I'm having trouble installing the lpsymphony package, using R-devel and devel branch of Bioconductor. Strange is that I've installed it successfully on this machine in the past.
First my sessionInfo:
R Under development (unstable) (2016-12-11 r71774) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.10 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] 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 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] 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_1.25.3 loaded via a namespace (and not attached): [1] compiler_3.4.0 tools_3.4.0
Below I paste the head and tail lend of the installation:
> biocLite("lpsymphony")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.3), R Under development (unstable)
(2016-12-11 r71774).
Installing package(s) ‘lpsymphony’
trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/lpsymphony_1.3.0.tar.gz'
Content type 'application/x-gzip' length 15716467 bytes (15.0 MB)
==================================================
downloaded 15.0 MB
* installing *source* package ‘lpsymphony’ ...
...
Master/master_func.c:1743:57: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
fscanf(f,"%s %s %i", str, str, &node->desc.desc_size);
^
Master/master_func.c:1748:23: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
fscanf(f, "%i", &ch);
^
Makefile:4188: recipe for target 'libSym_la-master_func.lo' failed
make[3]: *** [libSym_la-master_func.lo] Error 1
make[3]: Leaving directory '/tmp/RtmpYRREJw/R.INSTALL1dca245a0d9/lpsymphony/src/SYMPHONY/SYMPHONY/src'
Makefile:650: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/tmp/RtmpYRREJw/R.INSTALL1dca245a0d9/lpsymphony/src/SYMPHONY/SYMPHONY'
Makefile:324: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/tmp/RtmpYRREJw/R.INSTALL1dca245a0d9/lpsymphony/src/SYMPHONY'
Makevars:13: recipe for target 'SYMPHONY.ts' failed
make: *** [SYMPHONY.ts] Error 2
ERROR: compilation failed for package ‘lpsymphony’
* removing ‘/home/love/bin/R/library/lpsymphony’
The downloaded source packages are in
‘/tmp/RtmpHEzeex/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘lpsymphony’ had non-zero exit status
FWIW I wonder if what you've provided actually includes the error; they look like warnings that would not normally lead to an error.
Here's the first error:
In file included from ../include/sym_types.h:31:0, from ../include/sym_master.h:23, from Master/master_func.c:27: Master/master_func.c: In function ‘int set_param(sym_environment*, char*)’: ../include/sym_constants.h:334:1: error: ISO C++ forbids converting a string constant to ‘char*’ [-Wpedantic] } ^This may or may not help with the specific error; I pinged the maintainer so hopefully they will be by with some expert help.
Index: src/SYMPHONY/SYMPHONY/include/sym_types.h =================================================================== --- src/SYMPHONY/SYMPHONY/include/sym_types.h (revision 127018) +++ src/SYMPHONY/SYMPHONY/include/sym_types.h (working copy) @@ -286,7 +286,7 @@ typedef struct STR_INT{ #ifdef _OPENMP - char *str; + const char *str; #else char str[MAX_LINE_LENGTH +1]; #endifThat fixed it for me, thanks a lot!
This works for me as well, thanks.
It seems the problem made it into the 3.5 bioc release:
../include/sym_constants.h:358:1: error: ISO C++ forbids converting a string constant to 'char*' [-Wpedantic]
Is there any way to install it without patching the lpsymphony sources manually?
Hi Holger, can you please send me the output of your `R CMD config CFLAGS` and `R CMD config CXXFLAGS`?