error: Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL'
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dozhun • 0
@a106ca8c
Last seen 9 months ago
Hong Kong

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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 • 4.1k views
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1
Entering edit mode
Mike Smith ★ 5.7k
@mike-smith
Last seen 16 hours ago
EMBL Heidelberg / de.NBI

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.

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