[BioC] 回复： XVector

[Hervé Pagès]

On 09/10/2014 10:11 PM, libin wrote:
> Hi,
> My linux system can't network with the internet, so I download the
> XVector package.
> I use the commond install.packages("XVector_0.4.0.tar.gz").‍
> You mean it's the version problem?‍
> which version should I use?

It depends on what version of IRanges you have. biocLite() would
automatically figure out these things for you so I strongly recommend
that you use Bioconductor on a machine with internet access.

Cheers,
H.

>
> Best wishes.
> Bin
>
>
> ------------------ 原始邮件 ------------------
> *发件人:* "hpages";<hpages at fhcrc.org>;
> *发送时间:* 2014年9月11日(星期四) 中午12:29
> *收件人:* "libin"<skylib777 at gmail.com>;
> *抄送:* "bioconductor at r-project.org"<Bioconductor at r-project.org>;
> *主题:* Re: XVector
>
> 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
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319