CURLINFO_FILETIME_T not available in ubuntu 18.04

[js2264]

CURLINFO_FILETIME_T was added to curl in v. 7.59.0. Latest curl version available on Ubuntu 18.04 is 7.58.0, hence rtracklayer install fails on Ubuntu 18.04.

Some systems still rely on Ubuntu 18.04. FYI, rtracklayer install works on Ubuntu 18.04 by replacing the only occurence of CURLINFO_FILETIME_T by CURLINFO_FILETIME (here: https://github.com/lawremi/rtracklayer/blob/master/src/ucsc/net.c#L16). I don't know anything about curl so unsure how this would impact rtracklayer.

Of note, install also works by manually installing curl 7.59.0, of course.

This issue should be closed immediately if you are not planning on supporting Ubuntu 18.04 anymore. Otherwise let me know, I'd be happy to open a PR to change this.

BiocManager::install("rtracklayer") output:

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
Installing package(s) 'rtracklayer'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/rtracklayer_1.64.0.tar.gz'
Content type 'application/x-gzip' length 3951281 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

* installing *source* package 'rtracklayer' ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: 'gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0'

[...]

gcc -I"/usr/share/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/S4Vectors/include' -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/IRanges/include' -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/XVector/include'     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-U1b9am/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:255:5: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
     write(STDERR_FILENO, errMsg, strlen(errMsg));
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/share/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/S4Vectors/include' -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/IRanges/include' -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/XVector/include'     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-U1b9am/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/hash.c -o ucsc/hash.o

[...]

gcc -I"/usr/share/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/S4Vectors/include' -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/IRanges/include' -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/XVector/include'     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-U1b9am/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/udc.c -o ucsc/udc.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/S4Vectors/include' -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/IRanges/include' -I'/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/XVector/include'     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-U1b9am/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/net.c -o ucsc/net.o
In file included from /usr/include/x86_64-linux-gnu/curl/curl.h:2739:0,
                 from ucsc/net.c:7:
ucsc/net.c: In function 'header_get_last_modified':
ucsc/net.c:16:47: error: 'CURLINFO_FILETIME_T' undeclared (first use in this function); did you mean 'CURLINFO_FILETIME'?
     CURLcode status = curl_easy_getinfo(curl, CURLINFO_FILETIME_T, &last_modified);
                                               ^
ucsc/net.c:16:47: note: each undeclared identifier is reported only once for each function it appears in
make: *** [/usr/lib/R/etc/Makeconf:195: ucsc/net.o] Error 1
ERROR: compilation failed for package 'rtracklayer'
* removing '/home/rsg/R/x86_64-pc-linux-gnu-library/4.4/rtracklayer'

The downloaded source packages are in
        '/tmp/Rtmpj7uAy8/downloaded_packages'
Warning message:
In install.packages(...) :
  installation of package 'rtracklayer' had non-zero exit status

BiocManager::valid() output:

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org

* sessionInfo()

R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so;  LAPACK version 3.7.1

locale:
 [1] LC_CTYPE=en_IN.utf8        LC_NUMERIC=C               LC_TIME=en_IN.utf8         LC_COLLATE=en_IN.utf8      LC_MONETARY=en_IN.utf8    
 [6] LC_MESSAGES=en_IN.utf8     LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Paris
tzcode source: system (glibc)

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.23 compiler_4.4.0      tools_4.4.0        

Bioconductor version '3.19'

  * 1 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install("microbiomeDataSets", update = TRUE, ask = FALSE, force = TRUE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
1 packages out-of-date; 0 packages too new 

[lawremi]

Happy to look at a PR.

[jiananwehi]

I have the same problem when using R 4.4.0.

[drneavin]

I've run into the same issue with ubuntu 18.04 and R 4.4.0. Any solution for this?

[drneavin]

I fixed this in my case by manually installing curl v7.59.0 using the instructions here

[roxUCL]

Hi All, any update on this? I am facing the same issue on Ubuntu 18.04. I have also tried to install latest curl available (curl-8.3.0) but no luck.

Any help is very appreciated thanks

[drneavin]

It should be resolved if you downgrade your curl. I posted instructions I followed above

[roxUCL]

Thanks @drneavin but unfortunatelly this did not work either

[roxUCL]

sorted :) thanks

[JamesFrifan]

Hi. Thank you for fixing this. But I think I get a related error even if I am using the fixed version, which says:

[...] In file included from /usr/include/curl/curl.h:2251, from ucsc/net.c:7: ucsc/net.c: In function ‘header_get_content_length’: ucsc/net.c:40:47: error: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD_T’ undeclared (first use in this function); did you mean ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’? 40 | CURLcode status = curl_easy_getinfo(curl, CURLINFO_CONTENT_LENGTH_DOWNLOAD_T, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ucsc/net.c:40:47: note: each undeclared identifier is reported only once for each function it appears in ucsc/net.c: In function ‘netUrlOpenSockets’: ucsc/net.c:163:37: error: ‘CURLINFO_ACTIVESOCKET’ undeclared (first use in this function); did you mean ‘CURLINFO_LASTSOCKET’? 163 | curl_easy_getinfo(curl, CURLINFO_ACTIVESOCKET, &ctrlSocket); | ^~~~~~~~~~~~~~~~~~~~~ ucsc/net.c: In function ‘netSkipHttpHeaderLinesHandlingRedirect’: ucsc/net.c:204:29: error: ‘CURLINFO_ACTIVESOCKET’ undeclared (first use in this function); did you mean ‘CURLINFO_LASTSOCKET’? 204 | curl_easy_getinfo(curl, CURLINFO_ACTIVESOCKET, &nsd); | ^~~~~~~~~~~~~~~~~~~~~ make: *** [ucsc/net.o] Error 1 ERROR: compilation failed for package ‘rtracklayer’ [...]

I think this indicates that CURLINFO_CONTENT_LENGTH_DOWNLOAD_T (here: https://github.com/lawremi/rtracklayer/blob/master/src/ucsc/net.c#L40) should also be changed to CURLINFO_CONTENT_LENGTH_DOWNLOAD when using a lower version of curl.

Here is the related commit for curl: 3b80d3c

[hyein-cbio]

I happen to have a very old curl version, and I managed to install rtracklayer successfully in R 4.4. Could you check my take at the forked repository here? https://github.com/hyein-cbio/rtracklayer/commit/99945c88cd76e0dbe314168dd078652940ca4c30

[HeleneZhao]

hi, I am still not able to fixed this by manually installing curl v7.59.0. I am on Ubuntu 18.04 and R 4.4.0. Any help is much appreciated. curl --version curl 7.59.0 (x86_64-pc-linux-gnu) libcurl/8.3.0 OpenSSL/1.1.1 zlib/1.2.11 Release-Date: 2018-03-14 Protocols: dict file ftp ftps gopher gophers http https imap imaps mqtt pop3 pop3s rtsp smb smbs smtp smtps telnet tftp Features: AsynchDNS IPv6 Largefile NTLM NTLM_WB SSL libz TLS-SRP UnixSockets HTTPS-proxy But when I check in R

library(curl) Using libcurl 7.58.0 with OpenSSL/1.1.1

so I think there is something wrong with libcurl.

[lawremi]

@sanchit-saini would you be able to clean this up? If possible, please try to test it with the older libcurl (might be easiest in a container).

[sanchit-saini]

@lawremi okay, I will create a PR for it.