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Question: ERROR: dependency 'AnnotationDbi' is not available for package 'GO.db'
0
gravatar for Sidi.Ma
9 months ago by
Sidi.Ma0
the People's Republic of China/guangzhou/Sun Yat-sen university
Sidi.Ma0 wrote:

Hi , I'm a newcomer for R.  Recently I wanted to use GO.db in my windows 10 system. But I met a mistake during installation. Here is the mistake.

> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/GO.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 31897756 bytes (30.4 MB)
downloaded 30.4 MB

ERROR: dependency 'AnnotationDbi' is not available for package 'GO.db'
* removing 'D:/用户目录/我的文档/R/win-library/3.3/GO.db'

The downloaded source packages are in
    ‘C:\Users\Administrator\AppData\Local\Temp\Rtmp4ewGzV\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "D:\用户目录\我的文档\R\win-library\3.3" C:\Users\ADMINI~1\AppData\Local\Temp\Rtmp4ewGzV/downloaded_packages/GO.db_3.4.0.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status

When I use function traceback() to get the error. 

> traceback()
2: AnnotationDbi::as.data.frame()
1: AnnotationDbi::as.data.frame()

I have checked the "AnnotationDbi" package. Here is the consequence.

> sessionInfo("AnnotationDbi") 
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
character(0)

other attached packages:
[1] AnnotationDbi_1.36.2

loaded via a namespace (and not attached):
 [1] IRanges_2.8.1        BiocInstaller_1.24.0 graphics_3.3.2       DBI_0.5-1            parallel_3.3.2      
 [6] tools_3.3.2          utils_3.3.2          grDevices_3.3.2      memoise_1.0.0        Rcpp_0.12.9         
[11] stats_3.3.2          Biobase_2.34.0       datasets_3.3.2       RSQLite_1.1-2        S4Vectors_0.12.1    
[16] methods_3.3.2        digest_0.6.12        BiocGenerics_0.20.0  stats4_3.3.2         base_3.3.2    

 

What's wrong with this package? I have updated all the package, and the R is 3.3.2 version.

Thanks for any help in advance. 

ADD COMMENTlink modified 9 months ago • written 9 months ago by Sidi.Ma0
0
gravatar for Martin Morgan
9 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

R's dependency management system should have tried to install AnnotationDbi; but does it help to first say

biocLite("AnnotationDbi")

before trying GO.db?

ADD COMMENTlink written 9 months ago by Martin Morgan ♦♦ 20k

thanks for your help!

this is a method I have tried, but the reason is very unexpected. Just because a language problem.

thanks for your help again!

ADD REPLYlink written 9 months ago by Sidi.Ma0
0
gravatar for Sidi.Ma
9 months ago by
Sidi.Ma0
the People's Republic of China/guangzhou/Sun Yat-sen university
Sidi.Ma0 wrote:

OK, Now I have handled this question... Just because the default path of R's packages has chinese . A common mistake when running a non-chinese program in a chinese-based system. 

When I adjusted the default path to a  english path , this mistake disappeared..

ADD COMMENTlink modified 9 months ago • written 9 months ago by Sidi.Ma0
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