Question: Can't install GOSEQ (dependency problem) on CentOS 7!
0
gravatar for Raito92
4 weeks ago by
Raito9240
Italy
Raito9240 wrote:

Hello, I've tried to install the package goseq with:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("goseq")

But I get

* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
** libs
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c callbacks.c -o callbacks.o
gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c curl.c -o curl.o
gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c download.c -o download.o
gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c escape.c -o escape.o
gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c fetch.c -o fetch.o
gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c form.c -o form.o
gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c getdate.c -o getdate.o
gcc -std=gnu99 -I"/usr/local/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c handle.c -o handle.o
handle.c:30:1: error: unknown type name ‘curl_sslbackend’
 curl_sslbackend default_ssl_backend;
 ^
make: *** [handle.o] Errore 1
ERROR: compilation failed for package ‘curl’
* removing ‘/usr/local/lib64/R/library/curl’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/usr/local/lib64/R/library/httr’
ERROR: dependency ‘httr’ is not available for package ‘biomaRt’
* removing ‘/usr/local/lib64/R/library/biomaRt’
ERROR: dependency ‘biomaRt’ is not available for package ‘GenomicFeatures’
* removing ‘/usr/local/lib64/R/library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘geneLenDataBase’
* removing ‘/usr/local/lib64/R/library/geneLenDataBase’
ERROR: dependency ‘geneLenDataBase’ is not available for package ‘goseq’
* removing ‘/usr/local/lib64/R/library/goseq’

The downloaded source packages are in
        ‘/tmp/Rtmp1BgAoA/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘curl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘httr’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomicFeatures’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘geneLenDataBase’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘goseq’ had non-zero exit status

Here is my sessionInfo()

R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=it_IT.UTF-8
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=it_IT.UTF-8
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.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_1.30.4 compiler_3.5.3     tools_3.5.3

Any idea what could be wrong? Thanks in advance! If needed, I attach the whole log.

goseq R r package • 110 views
ADD COMMENTlink modified 4 weeks ago by Mike Smith4.0k • written 4 weeks ago by Raito9240

This seems to be a known issue with the curl package that has been reported here: https://github.com/jeroen/curl/issues/204

ADD REPLYlink written 4 weeks ago by shepherl ♦♦ 1.6k
Answer: Can't install GOSEQ (dependency problem) on CentOS 7!
2
gravatar for Mike Smith
4 weeks ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

I've encountered the same thing and worked around it by installing the previous version of the curl package via:

install.packages("https://cran.r-project.org/src/contrib/Archive/curl/curl_4.0.tar.gz", repo=NULL, type="source")

Not ideal, but it seems to work and allow the packages that depend on curl to be installed to.

ADD COMMENTlink written 4 weeks ago by Mike Smith4.0k
> install("curl")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'curl'
trying URL 'https://cran.rstudio.com/src/contrib/curl_4.1.tar.gz'
Content type 'application/x-gzip' length 667788 bytes (652 KB)
==================================================
downloaded 652 KB

<snip> 
gcc -std=gnu99 -I"/share/apps/R/R-3.6.0/lib64/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -I/usr/local/include -fvisibility=hidden -fpic  -g -O2  -c handle.c -o handle.o
handle.c:30:1: error: unknown type name curl_sslbackend
 curl_sslbackend default_ssl_backend;
 ^
make: *** [handle.o] Error 1
ERROR: compilation failed for package curl
< snip>
> system("curl --version", intern = TRUE)
[1] "curl 7.29.0 (x86_64-redhat-linux-gnu) libcurl/7.29.0 NSS/3.36 zlib/1.2.7 libidn/1.28 libssh2/1.4.3"                    
[2] "Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtsp scp sftp smtp smtps telnet tftp "
[3] "Features: AsynchDNS GSS-Negotiate IDN IPv6 Largefile NTLM NTLM_WB SSL libz unix-sockets "  

BUT

> library(BiocManager)
Bioconductor version 3.9 (BiocManager 1.30.4), ?BiocManager::install for help
> install("curl")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'curl'
<snip>

* DONE (curl)
< snip> 
> system("curl --version", intern = TRUE)
[1] "curl 7.54.0 (x86_64-unknown-linux-gnu) libcurl/7.54.0 GnuTLS/3.5.11 zlib/1.2.8"
[2] "Protocols: dict file ftp ftps gopher http https imap imaps pop3 pop3s rtsp smb smbs smtp smtps telnet tftp "
[3] "Features: IPv6 Largefile NTLM NTLM_WB SSL libz TLS-SRP UnixSockets HTTPS-proxy "
>

So an upgrade to a more recent curl version seems to do the trick.

ADD REPLYlink written 4 weeks ago by James W. MacDonald51k

I guess it depends if that's feasible. In my case the CentOS machine isn't administered by me, so controlling the system curl version gets challenging.

ADD REPLYlink written 4 weeks ago by Mike Smith4.0k

It's not that challenging though, is it? I don't have sudo privileges either, but it's inevitable that you are going to run into software that needs newer versions of whatever is installed (particularly if you are on a production OS like CentOS). I just install in my home dir:

git clone https://github.com/curl/curl.git
mkdir /home/jmacdon/programs
cd curl
./config --prefix=/home/jmacdon/programs
make; make install
## edit .bashrc to include
export PKG_CONFIG_PATH=/home/jmacdon/programs/lib/pkgconfig:$PKG_CONFIG_PATH

after which curl installs no problem.

ADD REPLYlink written 4 weeks ago by James W. MacDonald51k

This solved the problem, thank you!

ADD REPLYlink written 27 days ago by Raito9240
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