error: Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL'
1
0
Entering edit mode
dozhun • 0
@a106ca8c
Last seen 2.4 years ago
Hong Kong

Enter the body of text here

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

hi,
when I load package like DESeq2 or AnnotatiobDbi, return massage like below, I has tried search the error information according Google, but didn't saved, any one hvae resolve methods? Thanks!


>BiocManager::install("AnnotationDbi", force = T)
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'AnnotationDbi'
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/AnnotationDbi_1.56.1.tar.gz'
Content type 'application/x-gzip' length 4329593 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

* installing *source* package ‘AnnotationDbi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** help
*** installing help indices
  converting help for package ‘AnnotationDbi’
    finding HTML links ... done
    AnnDbObj-class                          html  
    AnnDbPkg-checker                        html  
    AnnotationDb-class                      html  
    AnnotationDbi-internals                 html  
    Bimap-direction                         html  
    Bimap-envirAPI                          html  
    Bimap-keys                              html  
    Bimap-toTable                           html  
    Bimap                                   html  
    BimapFiltering                          html  
    BimapFormatting                         html  
    GOColsAndKeytypes                       html  
    GOFrame                                 html  
    GOTerms-class                           html  
    KEGGFrame                               html  
    colsAndKeytypes                         html  
    createSimpleBimap                       html  
    inpIDMapper                             html  
    makeGOGraph                             html  
    make_eg_to_go_map                       html  
    orgPackageName                          html  
    organismKEGGFrame                       html  
    print.probetable                        html  
    toSQLStringSet                          html  
    unlist2                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AnnotationDbi)

The downloaded source packages are in
    ‘/tmp/RtmpNAS4cO/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /opt/R/4.1.0/lib/R/library
  packages:
    lattice, Matrix, mgcv, nlme, survival
>> library(AnnotationDbi)
Error: package or namespace load failed for ‘AnnotationDbi’:
 .onLoad failed in loadNamespace() for 'httr', details:
  call: options()
  error: Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL'

sessionInfo(R-4.1.0 )
PackageLoading • 7.4k views
ADD COMMENT
1
Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 22 hours ago
EMBL Heidelberg

Looks like you're experiencing the same error seen in Error arrayQualityMetrics

The solution there was to make sure you've got a working copy of httr by installing the package again using install.packages("httr"). Then restart R and try loading AnnotationDbi again.

ADD COMMENT

Login before adding your answer.

Traffic: 629 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