Dependencies not available for package (Ubuntu and Fedora)

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When checking a new package envi on Ubuntu and Fedora, a PREPERROR is issued because dependencies cannot be installed.

On Ubuntu Linux there are problems with concaveman and sf.

4048#> ERROR: dependency ‘sf’ is not available for package ‘concaveman’

On Fedora Linux there are problems with concaveman, sf, V8, rgeos, xm12, and units

3390#> ERROR: dependencies ‘V8’, ‘sf’ are not available for package ‘concaveman’

2824#> checking for geos-config... no 2825#> no 2826#> configure: error: geos-config not found or not executable. 2827#> ERROR: configuration failed for package ‘rgeos’

2210#> Using PKG_LIBS=-lxml2 2211#> ------------------------- ANTICONF ERROR --------------------------- 2212#> Configuration failed because libxml-2.0 was not found. Try installing: 2213#> * deb: libxml2-dev (Debian, Ubuntu, etc) 2214#> * rpm: libxml2-devel (Fedora, CentOS, RHEL) 2215#> * csw: libxml2_dev (Solaris) 2216#> If libxml-2.0 is already installed, check that 'pkg-config' is in your 2217#> PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config 2218#> is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: 2219#> R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' 2220#> -------------------------------------------------------------------- 2221#> ERROR: configuration failed for package ‘xml2’

2316#> checking for ut_read_xml in -ludunits2... no 2317#> configure: error: in '/tmp/RtmpdnuGTG/R.INSTALL157717ee494c/units': 2318#> configure: error: 2319#> -------------------------------------------------------------------------------- 2320#> Configuration failed because libudunits2.so was not found. Try installing: 2321#> * deb: libudunits2-dev (Debian, Ubuntu, ...) 2322#> * rpm: udunits2-devel (Fedora, EPEL, ...) 2323#> * brew: udunits (OSX) 2324#> If udunits2 is already installed in a non-standard location, use: 2325#> --configure-args='--with-udunits2-lib=/usr/local/lib' 2326#> if the library was not found, and/or: 2327#> --configure-args='--with-udunits2-include=/usr/include/udunits2' 2328#> if the header was not found, replacing paths with appropriate values. 2329#> You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually. 2330#> -------------------------------------------------------------------------------- 2331#> See `config.log' for more details 2332#> ERROR: configuration failed for package ‘units’

The logs can be checked for: Fedora Linux, R-devel, clang, gfortran Ubuntu Linux 16.04 LTS, R-release, GCC Ubuntu Linux 16.04 LTS, R-release, GCC

[thijsjanzen]

This issue also arises when checking on Solaris (https://builder.r-hub.io/status/original/GenomeAdmixR_1.1.2.tar.gz-0bd720be406c4121a3b4a38d190565e3), where a whole range of package dependencies fails (hierfstat, adegenet, spdep, sf, units), because the units package cannot install due to:

configure: error: in `/export/home/XHxxvIH/Rtemp/RtmpkZIVmK/R.INSTALL2df4695f2ada/units':
configure: error: 
--------------------------------------------------------------------------------
  Configuration failed because libudunits2.so was not found. Try installing:
    * deb: libudunits2-dev (Debian, Ubuntu, ...)
    * rpm: udunits2-devel (Fedora, EPEL, ...)
    * brew: udunits (OSX)
  If udunits2 is already installed in a non-standard location, use:
    --configure-args='--with-udunits2-lib=/usr/local/lib'
  if the library was not found, and/or:
    --configure-args='--with-udunits2-include=/usr/include/udunits2'
  if the header was not found, replacing paths with appropriate values.
  You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
--------------------------------------------------------------------------------

[gaborcsardi]

The units package seems to work on CRAN's Solaris, so they probably have the system requirements installed. We'll look into that on our Solaris server as well.

[dpprdan]

Nevermind, my problem is not related to this, but https://github.com/r-hub/rhub/issues/361#issuecomment-635482750

~~I get couldn't-install-sf errors on Fedora as well:~~ ~~See:~~ ~~https://builder.r-hub.io/status/opencage_0.2.0.tar.gz-de526489d1ab46bb93499be21f12146c#L2331~~ ~~https://builder.r-hub.io/status/opencage_0.2.0.tar.gz-9ba591a1ebed441f98d7fa95f1c71607#L2347~~

[loreabad6]

Is there any update on the units package on the Solaris server? I am getting the same problem here: https://builder.r-hub.io/status/sfnetworks_0.5.0.tar.gz-52f47c1f1cbb41aa8624bb8e3fbbc77d

[gaborcsardi]

@loreabad6 The udunits does not compile on Solaris, so it is unlikely that there will be any progress.

[gaborcsardi]

@loreabad6 Managed to package up udunits for Solaris, so the units package installs now.

There is still no recent enough gdal, though, that would allow installing rgdal or sf.

[loreabad6]

so the units package installs now.

Thank you!

There is still no recent enough gdal, though, that would allow installing rgdal or sf.

I see. Is it then also not possible to test locally with the Solaris VM as mentioned here?

I have not tested yet.

[gaborcsardi]

Managed to compile a newer libgeos and libgdal, so sf and co. now works on R-hub's Solaris machine.

[laresbernardo]

Having this same issue here.

#> * installing *source* package ‘curl’ ...
2421#> ** package ‘curl’ successfully unpacked and MD5 sums checked
2422#> ** using staged installation
2423#> Package libcurl was not found in the pkg-config search path.
2424#> Perhaps you should add the directory containing `libcurl.pc'
2425#> to the PKG_CONFIG_PATH environment variable
2426#> Package 'libcurl', required by 'virtual:world', not found
2427#> Package libcurl was not found in the pkg-config search path.
2428#> Perhaps you should add the directory containing `libcurl.pc'
2429#> to the PKG_CONFIG_PATH environment variable
2430#> Package 'libcurl', required by 'virtual:world', not found
2431#> Using PKG_CFLAGS=
2432#> Using PKG_LIBS=-lcurl
2433#> ------------------------- ANTICONF ERROR ---------------------------
2434#> Configuration failed because libcurl was not found. Try installing:
2435#> * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
2436#> * rpm: libcurl-devel (Fedora, CentOS, RHEL)
2437#> * csw: libcurl_dev (Solaris)
2438#> If libcurl is already installed, check that 'pkg-config' is in your
2439#> PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
2440#> is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
2441#> R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
2442#> --------------------------------------------------------------------
2443#> ERROR: configuration failed for package ‘curl’
2444#> * removing ‘/home/docker/R/curl’

[gaborcsardi]

This issue is about the previous R-hub system, it does not apply to the new system, so I am closing it now. Please see https://r-hub.github.io/rhub/ for the new system, R-hub v2.