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