ERROR: dependency 'AnnotationDbi' is not available for package 'GO.db'
2
0
Entering edit mode
Sidi.Ma • 0
@sidima-12420
Last seen 7.8 years ago
the People's Republic of China/guangzho…

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. 

bioconductor R go.db annotationdbi dependency • 4.5k views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 4 months ago
United States

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode
Sidi.Ma • 0
@sidima-12420
Last seen 7.8 years ago
the People's Republic of China/guangzho…

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 COMMENT

Login before adding your answer.

Traffic: 666 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6