DESeq2 installation error
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Entering edit mode
Norbert ▴ 10
@a5fb06e6
Last seen 13 months ago
Hungary

I tried to install DESeq2 with this code:

BiocManager::install("DESeq2")

I got error like this:

 Error: package or namespace load failed for ‘curl’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-curl/00new/curl/libs/curl.so':
  /home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-curl/00new/curl/libs/curl.so: undefined symbol: curl_easy_option_next
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/curl’
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /bin/sed
checking for pkg-config... /home/linuxbrew/.linuxbrew/bin/pkg-config
checking for xml2-config... /home/linuxbrew/.linuxbrew/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 10, Patch 3 for 2.10.3
Located parser file -I/home/linuxbrew/.linuxbrew/Cellar/libxml2/2.10.3_2/include/libxml2/parser.h
Checking for 1.8:  -I/home/linuxbrew/.linuxbrew/Cellar/libxml2/2.10.3_2/include/libxml2
Using libxml2.*
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... no
checking for xmlParseFile in -lxml... no
configure: error: "libxml not found"
ERROR: configuration failed for package ‘XML’
* removing ‘/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/XML’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/httr’
ERROR: dependency ‘httr’ is not available for package ‘KEGGREST’
* removing ‘/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/KEGGREST’
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
* removing ‘/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/AnnotationDbi’
ERROR: dependencies ‘AnnotationDbi’, ‘XML’, ‘httr’ are not available for package ‘annotate’
* removing ‘/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/annotate’
ERROR: dependencies ‘annotate’, ‘AnnotationDbi’ are not available for package ‘geneplotter’
* removing ‘/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/geneplotter’
ERROR: dependency ‘geneplotter’ is not available for package ‘DESeq2’
* removing ‘/home/gulyas/R/x86_64-pc-linux-gnu-library/4.2/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmphJgjXt/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘curl’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘XML’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘httr’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘KEGGREST’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘AnnotationDbi’ had non-zero exit status
6: In install.packages(...) :
  installation of package ‘annotate’ had non-zero exit status
7: In install.packages(...) :
  installation of package ‘geneplotter’ had non-zero exit status
8: In install.packages(...) :
  installation of package ‘DESeq2’ had non-zero exit status



sessionInfo( )

R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=hu_HU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=hu_HU.UTF-8        LC_COLLATE=hu_HU.UTF-8    
 [5] LC_MONETARY=hu_HU.UTF-8    LC_MESSAGES=hu_HU.UTF-8   
 [7] LC_PAPER=hu_HU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=hu_HU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.19 compiler_4.2.2      tools_4.2.2 

Could you suggest any solution to resolve this error?

DESeq2 • 1.0k views
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The initial failure is in the curl install. I came across this post as we had a bug report against our software yesterday which seems to be the same curl failure. For some reason it's not able to load the binary which it's just compiled. I can't find any other references to this curl_easy_option_next symbol other than this post, which is suspiciously new, so I suspect something has changed either in a recent curl release, or in a curl library on whichever OS you're using.

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for "curl" in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/[username]/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-curl/00new/curl/libs/curl.so':
  /home/[username]/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-curl/00new/curl/libs/curl.so: undefined symbol: curl_easy_option_next
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shepherl 3.8k
@lshep
Last seen 15 hours ago
United States

Looks like your missing a system dependency libxml not found . Try installing with something like sudo apt-get install libxml2-dev

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Entering edit mode

Thank you for your answer.

I tried install the libxml2-dev but ubuntu said that this package is already installed.

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maybe this article might be useful (towards the end it goes into its already installed but not being found): https://community.rstudio.com/t/can-not-install-xml-package/48854

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