rhdf5 installtion fails on Debian 8 due to compilation errors
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Entering edit mode
ch.diener • 0
@chdiener-11431
Last seen 5.1 years ago

Installing rhd5 via the recommended version fails on Debian 8 with R 3.3.1.

In file included from /usr/share/R/include/R.h:40:0,
                 from HandleList.h:4,
                 from HandleListcpp.h:11,
                 from HandleList.cpp:2:
/usr/include/c++/4.9/cstdlib: In function ‘long long int std::abs(long long int)’:
/usr/include/c++/4.9/cstdlib:174:20: error: conflicting declaration of C function ‘long long int std::abs(long long int)’
   abs(long long __x) { return __builtin_llabs (__x); }

<font face="monospace">There are many more of those... and finally:</font>

usr/lib/R/etc/Makeconf:141: recipe for target 'HandleList.o' failed
make: *** [HandleList.o] Error 1
ERROR: compilation failed for package ‘rhdf5’

Session Info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

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_1.20.3

loaded via a namespace (and not attached):
[1] tools_3.3.1

 

 

rhdf5 • 916 views
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0
Entering edit mode
ch.diener • 0
@chdiener-11431
Last seen 5.1 years ago

Updating Bioconductor to 3.3 fixed this. So if you are encountering the same error:

remove.packages("BiocInstaller")
source("https://bioconductor.org/biocLite.R")
biocLite() 

Cheers

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