Hello,
I am using 4.1.1 version of R and 3.13 version of Bioconductor and there is no way to install AnnotationHub package. I think there is general problem with package installations.
After using the command BiocManager::install("AnnotationHub"), I get following error message:
ERROR: configuration failed for package ‘curl’
* removing ‘/home/teki/R/x86_64-pc-linux-gnu-library/4.1/curl’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/teki/R/x86_64-pc-linux-gnu-library/4.1/GenomeInfoDb’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/teki/R/x86_64-pc-linux-gnu-library/4.1/httr’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’
* removing ‘/home/teki/R/x86_64-pc-linux-gnu-library/4.1/Biostrings’
ERROR: dependencies ‘curl’, ‘httr’ are not available for package ‘BiocFileCache’
* removing ‘/home/teki/R/x86_64-pc-linux-gnu-library/4.1/BiocFileCache’
ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’
* removing ‘/home/teki/R/x86_64-pc-linux-gnu-library/4.1/KEGGREST’
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
* removing ‘/home/teki/R/x86_64-pc-linux-gnu-library/4.1/AnnotationDbi’
ERROR: dependencies ‘BiocFileCache’, ‘curl’, ‘AnnotationDbi’, ‘httr’ are not available for package ‘AnnotationHub’
* removing ‘/home/teki/R/x86_64-pc-linux-gnu-library/4.1/AnnotationHub’
The downloaded source packages are in
‘/tmp/RtmpOG7MjX/downloaded_packages’
Installation paths not writeable, unable to update
packages
path: /usr/lib/R/library
packages:
nlme, spatial
path: /usr/lib/R/site-library
packages:
BH
Warning messages:
1: In .inet_warning(msg) :
installation of package ‘RCurl’ had non-zero exit status
2: In .inet_warning(msg) :
installation of package ‘curl’ had non-zero exit status
3: In .inet_warning(msg) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
4: In .inet_warning(msg) :
installation of package ‘httr’ had non-zero exit status
5: In .inet_warning(msg) :
installation of package ‘Biostrings’ had non-zero exit status
6: In .inet_warning(msg) :
installation of package ‘BiocFileCache’ had non-zero exit status
7: In .inet_warning(msg) :
installation of package ‘KEGGREST’ had non-zero exit status
8: In .inet_warning(msg) :
installation of package ‘AnnotationDbi’ had non-zero exit status
9: In .inet_warning(msg) :
installation of package ‘AnnotationHub’ had non-zero exit status
Do you have any advice what to do? I have tried a lot of suggestion I came upon while googling but they are all regarding older versions of R and are not helpful.
Please, if you have any ideas I'll be willing to try them!
Thank you so much! However, I have already tried this and after running the command install.packages("RCurl") I get the following error message:
checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ‘RCurl’
The downloaded source packages are in ‘/tmp/RtmpOG7MjX/downloaded_packages’
I tried to install curl now as you said, but on terminal I get this message: "curl is already the newest version (7.68.0-1ubuntu2.7)." "0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded." and RCurl is still failing to install.
If you have any other suggestions please help, and thank you once again for your time and advice!!
Sorry for the interruption, thanks to you I managed to figure it out! I just had to install curl by sudo apt install libcurl4-openssl-dev on terminal. AnnotationHub is installed. Thanks again.