[BioC] XVector

[Hervé Pagès]

Hi,

You're not showing the command you used to install XVector.
Remember that you should *always* use biocLite() to install
a Bioconductor package, as explained here:

   http://bioconductor.org/install/

This avoids version mismatches, which is probably what is
happening in your case.

Hope this helps,

H.

On 09/10/2014 08:28 PM, libin wrote:
> hi,Pages‍
> I met a problem when install the R package "XVector "
> the error messages are as follows:
> my R version is 3.1.1, can you give me some tips?
> thank you!
>
> gcc -std=gnu99
> -I/ifshk4/BC_CANCER/PROJECT/HKC11045_HUMxfnX_EC/zhouyong/libin01/R/R-3.1.1/include
> -DNDEBUG  -I/usr/local/include
> -I"/ifshk4/BC_CANCER/PROJECT/HKC11045_HUMxfnX_EC/zhouyong/libin01/R/R-3.1.1/library/IRanges/include"
>    -fpic  -g -O2  -c SharedVector_class.c -o SharedVector_class.o
> SharedVector_class.c: In function 'SharedVector_memcmp':
> SharedVector_class.c:237: warning: implicit declaration of function
> 'vector_memcmp'
> gcc -std=gnu99
> -I/ifshk4/BC_CANCER/PROJECT/HKC11045_HUMxfnX_EC/zhouyong/libin01/R/R-3.1.1/include
> -DNDEBUG  -I/usr/local/include
> -I"/ifshk4/BC_CANCER/PROJECT/HKC11045_HUMxfnX_EC/zhouyong/libin01/R/R-3.1.1/library/IRanges/include"
>    -fpic  -g -O2  -c XRawList_comparison.c -o XRawList_comparison.o
> XRawList_comparison.c:284: warning: 'struct htab' declared inside
> parameter list
> XRawList_comparison.c:284: warning: its scope is only this definition or
> declaration, which is probably not what you want
> XRawList_comparison.c: In function 'get_bucket_idx_for_Chars_holder':
> XRawList_comparison.c:292: error: dereferencing pointer to incomplete type
> XRawList_comparison.c:293: error: dereferencing pointer to incomplete type
> XRawList_comparison.c:298: error: dereferencing pointer to incomplete type
> XRawList_comparison.c: In function 'XRawList_match_hash':
> XRawList_comparison.c:309: error: storage size of 'htab' isn't known
> XRawList_comparison.c:317: warning: implicit declaration of function
> 'new_htab'
> XRawList_comparison.c:322: warning: implicit declaration of function
> 'get_hbucket_val'
> XRawList_comparison.c:323: warning: implicit declaration of function
> 'set_hbucket_val'
> XRawList_comparison.c: In function 'XRawList_selfmatch_hash':
> XRawList_comparison.c:347: error: storage size of 'htab' isn't known
> make: *** [XRawList_comparison.o] Error 1
> ERROR: compilation failed for package 'XVector'
> * removing
> '/ifshk4/BC_CANCER/PROJECT/HKC11045_HUMxfnX_EC/zhouyong/libin01/R/R-3.1.1/library/XVector'
> Warning message:
> In install.packages("XVector_0.4.0.tar.gz") :
>    installation of package 'XVector_0.4.0.tar.gz' had non-zero exit status‍
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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