[Bioc-devel] Rsubread build error

Wei Shi shi at wehi.EDU.AU
Fri Mar 29 12:00:58 CET 2013


Hi Martin and Dan,

Thanks for your help. Although we do not have any errors in building Rsubead on our linux machine, I have incorporated all the changes you suggested into Rsubread. I tested it on our machine and it worked fine. I have just committed the changes to the devel svn repository and the latest Rsubread version is 1.9.7. Hope it now works on george2.

The version of R I'm using is R3.0.0rc r62427.


Best regards,

Wei




On Mar 29, 2013, at 3:08 PM, Martin Morgan wrote:

> On 03/28/2013 08:36 PM, Wei Shi wrote:
>> Dear Bioc core team,
>> 
>> Our Rsubead package got a build error on george2, but we could not reproduce the error on our local linux machine. It is successfully built and installed on our linux computer. Is it possible that you can give us more information about what might cause this error?
>> 
> 
> Hi Wei -
> 
> The configure file fails
> 
> ./configure: 9: ./configure: [[: not found
> 
> so the wrong Makefile is being used. You need to link to libz
> 
> $ svn diff Makevars.Linux
> Index: Makevars.Linux
> ===================================================================
> --- Makevars.Linux	(revision 74972)
> +++ Makevars.Linux	(working copy)
> @@ -1,2 +1,2 @@
> PKG_CFLAGS+=-DMAKE_FOR_EXON
> -PKG_LIBS+=-lpthread -DMAKE_FOR_EXON
> +PKG_LIBS+=-lz -lpthread -DMAKE_FOR_EXON
> 
> 
> 'inline' functions need to be declared 'static'
> 
> 
> $ svn diff sorted-hashtable.c
> Index: sorted-hashtable.c
> ===================================================================
> --- sorted-hashtable.c	(revision 74972)
> +++ sorted-hashtable.c	(working copy)
> @@ -851,7 +851,7 @@
> // }
> //
> 
> -inline unsigned int load_int32(FILE * fp)
> +static inline unsigned int load_int32(FILE * fp)
> {
> 	int ret;
> 	int read_length;
> @@ -860,7 +860,7 @@
> 	return ret;
> }
> 
> -inline long long int load_int64(FILE * fp)
> +static inline long long int load_int64(FILE * fp)
> {
> 	long long int ret;
> 	int read_length;
> 
> 
>> Many thanks,
>> Wei
>> 
>> ______________________________________________________________________
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>> 
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>> 
> 
> 
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> 
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