Trouble installing rhdf5 on opensuse
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Entering edit mode
@johannesgudbrandsson-12285
Last seen 4.7 years ago

Hi 

I have had problem installing rhdf on opnesuse (leap 42.1). It has something to do with the c++ source code. I could not post the complete message from the installer but it can be seen here https://notendur.hi.is/jog7/error_rhdf.txt

An example of the errors can be seen below.

Thanks

Jóhannes

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 42.1 (x86_64)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=is_IS.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=is_IS.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=is_IS.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=is_IS.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  base     
> biocLite("rhdf5")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.2 (2016-10-31).
Installing package(s) ‘rhdf5’
trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/rhdf5_2.14.0.tar.gz'
Content type 'unknown' length 5390037 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

* ** Skipping alot****

In file included from /usr/lib64/R/include/R.h:40:0,
                 from HandleList.h:4,
                 from HandleListcpp.h:11,
                 from HandleList.cpp:2:
/usr/include/c++/4.8/cstdlib: In function ‘long long int std::abs(long long int)’:
/usr/include/c++/4.8/cstdlib:174:20: error: declaration of C function ‘long long int std::abs(long long int)’ conflicts with
   abs(long long __x) { return __builtin_llabs (__x); }
                    ^
/usr/include/c++/4.8/cstdlib:166:3: error: previous declaration ‘long int std::abs(long int)’ here
   abs(long __i) { return __builtin_labs(__i); }
   ^
/usr/include/c++/4.8/cstdlib: In function ‘__int128 std::abs(__int128)’:
/usr/include/c++/4.8/cstdlib:179:19: error: declaration of C function ‘__int128 std::abs(__int128)’ conflicts with
   abs(__int128 __x) { return __x >= 0 ? __x : -__x; }
                   ^
/usr/include/c++/4.8/cstdlib:174:3: error: previous declaration ‘long long int std::abs(long long int)’ here
   abs(long long __x) { return __builtin_llabs (__x); }
   ^
/usr/include/c++/4.8/cstdlib:179:19: error: declaration of C function ‘__int128 std::abs(__int128)’ conflicts with
   abs(__int128 __x) { return __x >= 0 ? __x : -__x; }
                   ^
/usr/include/c++/4.8/cstdlib:166:3: error: previous declaration ‘long int std::abs(long int)’ here
   abs(long __i) { return __builtin_labs(__i); }
   ^
In file included from /usr/lib64/R/include/R.h:43:0,
                 from HandleList.h:4,
                 from HandleListcpp.h:11,
                 from HandleList.cpp:2:
/usr/include/c++/4.8/cmath: In function ‘double std::abs(double)’:
/usr/include/c++/4.8/cmath:81:17: error: declaration of C function ‘double std::abs(double)’ conflicts with
   abs(double __x)
                 ^
In file included from /usr/lib64/R/include/R.h:40:0,
                 from HandleList.h:4,
                 from HandleListcpp.h:11,
                 from HandleList.cpp:2:
and many many more 
rhdf5 opensuse • 880 views
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0
Entering edit mode
@johannesgudbrandsson-12285
Last seen 4.7 years ago

Hi

I was able to install after I updated R and bioconductor.

Cheers

Jóhannes

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