DESeq2 installation error
1
0
Entering edit mode
Norbert ▴ 10
@a5fb06e6
Last seen 21 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 • 1.5k views
ADD COMMENT
0
Entering edit mode

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
ADD REPLY
0
Entering edit mode
shepherl 4.1k
@lshep
Last seen 2 days ago
United States

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

ADD COMMENT
0
Entering edit mode

Thank you for your answer.

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 506 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