Search
Question: org.Hs.eg.db loadNamespace() error
0
gravatar for alok.jaiswal
2.3 years ago by
alok.jaiswal0 wrote:

I am trying to install the latest org.Hs.eg.db package but I get the following error. Any ideas on how to deal with this ?

install.packages("org.Hs.eg.db_3.1.2.tar.gz", repos = NULL, type = "source")

Installing package into ‘/Users/jaiswal/Library/R/3.1/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘org.Hs.eg.db’ ...
** R
** inst
** preparing package for lazy loading
Warning: package ‘AnnotationDbi’ was built under R version 3.2.0
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for class “Annotated” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “DataFrame” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “DataTable” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “DataTableORNULL” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “Hits” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “List” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “Rle” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “SimpleList” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “Vector” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “characterORNULL” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “vectorORfactor” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “xtabs” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Warning: multiple methods tables found for ‘width’
Warning: multiple methods tables found for ‘start<-’
Warning: multiple methods tables found for ‘width<-’
Warning: multiple methods tables found for ‘end<-’
Warning: multiple methods tables found for ‘score’
Warning: multiple methods tables found for ‘score<-’
Warning: multiple methods tables found for ‘unsplit’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: package ‘AnnotationDbi’ was built under R version 3.2.0
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Note: the specification for class “Annotated” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “DataFrame” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “DataTable” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “DataTableORNULL” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “Hits” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “List” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “Rle” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “SimpleList” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “Vector” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “characterORNULL” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “vectorORfactor” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for S3 class “xtabs” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Warning: multiple methods tables found for ‘width’
Warning: multiple methods tables found for ‘start<-’
Warning: multiple methods tables found for ‘width<-’
Warning: multiple methods tables found for ‘end<-’
Warning: multiple methods tables found for ‘score’
Warning: multiple methods tables found for ‘score<-’
Warning: multiple methods tables found for ‘unsplit’
Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: ls(ann_objs)
  error: could not find symbol "sorted" in environment of the generic function
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/jaiswal/Library/R/3.1/library/org.Hs.eg.db’
* restoring previous ‘/Users/jaiswal/Library/R/3.1/library/org.Hs.eg.db’
Warning in install.packages :
  installation of package ‘org.Hs.eg.db_3.1.2.tar.gz’ had non-zero exit status

 

 

ADD COMMENTlink modified 2.3 years ago by Martin Morgan ♦♦ 20k • written 2.3 years ago by alok.jaiswal0
0
gravatar for Martin Morgan
2.3 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

Bioconductor packages are tied to particular R versions. You're installing a new package on an old version. I think though that actually the problem is not with the org package, but AnnotationDbi, where I think you have installed a (binary) version meant to work with R-3.2 in your version of R-3.1. Maybe you copied the installed AnnotationDbi from one library to the other? This is only a guess; the underlying problem is I think version mis-matches. You could try BiocInstaller::biocValid() and follow the advice to try and sort things out, and then only install packages with biocLite("org.Hs.eg.db") to avoid this problem in the future. If the end goal is to use the most recent org package, then you need to use the most recent R, version 3.2.1.

ADD COMMENTlink written 2.3 years ago by Martin Morgan ♦♦ 20k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 251 users visited in the last hour