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Question: lpsymphony install on Ubuntu
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gravatar for Michael Love
9 months ago by
Michael Love15k
United States
Michael Love15k wrote:

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
ADD COMMENTlink modified 9 months ago • written 9 months ago by Michael Love15k

FWIW I wonder if what you've provided actually includes the error; they look like warnings that would not normally lead to an error.

ADD REPLYlink written 9 months ago by Martin Morgan ♦♦ 20k
I tried to include more of the compilation but got clipped by support site. I didn't see anything suspicious in the clipped part. I guess, I'm hoping someone also on Ubuntu 16.10 and devel branch might have seen this already.
ADD REPLYlink modified 9 months ago • written 9 months ago by Michael Love15k

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]
 }
 ^
ADD REPLYlink written 9 months ago by Michael Love15k
1

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];
 #endif

 

ADD REPLYlink written 9 months ago by Martin Morgan ♦♦ 20k

That fixed it for me, thanks a lot!

ADD REPLYlink written 8 months ago by gokcen.eraslan10

This works for me as well, thanks.

ADD REPLYlink written 8 months ago by Michael Love15k

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?

ADD REPLYlink written 5 months ago by holgerbrandl10

Hi Holger, can you please send me the output of your `R CMD config CFLAGS` and `R CMD config CXXFLAGS`? 

 

 

 

 

ADD REPLYlink written 5 months ago by vladislav.kim10
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