Running under: CentOS Linux 7 (Core), Matrix products: default Thanks! I started with a fresh copy of the LibIIO repo and re-ran cmake. Have a question about this project? Scanning dependencies of target iio Stack Exchange network consists of 181 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. I am trying to install the XML package via BiocLite, which I need for various other packages. Asking for help, clarification, or responding to other answers. In file included from /usr/include/libxml2/libxml/parser.h:810:0, You have to ignore the suggestion from pgModeler documentation. symbols will now be hidden. You can get all the above info by running: it will tell you the full paths to all the files in that package. You signed in with another tab or window. https://webkaru.net/linux/configure-error-xml2-config-found-please-check-libxml2-installation/, https://stackoverflow.com/questions/45775877/configure-error-please-reinstall-the-libzip-distribution. In your case, you are probably missing the libxml2-dev package. -- The C compiler identification is GNU 7.4.0 What did help was to install libxml through conda using. to your account. How a top-ranked engineering school reimagined CS curriculum (Ep. one patches configure.ac and can then run autoreconf. CMakeFiles/iio.dir/build.make:302: recipe for target 'CMakeFiles/iio.dir/xml.c.o' failed checking whether gcc accepts -g yes Working PATH (for me): /usr/local/sbin:/usr/local/bin:/usr/bin:/var/lib/flatpak/exports/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl. issues see https://gitlab.gnome.org/GNOME/libxml2/-/issues/507, Powered by Discourse, best viewed with JavaScript enabled, https://download.gnome.org/sources/libxml2/2.11/libxml2-2.11.0.tar.xz, https://gitlab.gnome.org/GNOME/libxml2/-/issues/507. For a list of important open So how can i add libxml-2.0.pc in /usr/lib/pkgconfig/. https://download.gnome.org/sources/libxml2/2.11/libxml2-2.11.0.tar.xz (2.50M) but an incompatible library. installed. which indicates to me that /usr/lib/x86_64-linux-gnu/pkgconfig is already in the default path for pkg-config. During the ./configure it will produce the following error: However I do have libxslt installed, e.g. * should still be possible to run binaries linked against older versions. What differentiates living as mere roommates from living in a marriage-like relationship? Learn more about Stack Overflow the company, and our products. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. Hello- I found this discussion on the mailing list archives: >On Fri, 6 Oct 2000, Pallentin wrote: >> Hi there, >> I try to install ver. so I'm trying to use pkg-config, as it suggests but then getting the new error: /app/INSTALL_FILES/pkg-config-.29.2 # ./configure --with-internal-glib but I get this error when I try 'make' command: # CC=gcc # export CC # make make Looks like the new markdown functionality is affecting the last section`# Install XML` with an `a href` tags, but looks normal when I try to edit the post. I'm trying to figure out what needs to be done to make the configure script happy with libxml2 because libxml-2.0 isn't available. Find centralized, trusted content and collaborate around the technologies you use most. So what include directory does CMake uses for libxml2? Can you still use Commanders Strike if the only attack available to forego is an attack against an ally? I had already pkg-config installed but the path was pointing to correct location (AWS instance). * checking for gzopen in -lz. This should also work as I didn't have brew: So, you already have libxml2 installed with brew. -- Looking for strerror_r Then running pkg-config --variable pc_path pkg-config gives (my highlighting): /usr/local/lib/x86_64-linux-gnu/pkgconfig:/usr/local/lib/pkgconfig:/usr/local/share/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/lib/pkgconfig:/usr/share/pkgconfig. Can someone explain why this point is giving me 8.3V? checking for suffix of executables Here are my steps and the results. [ 19%] Building C object CMakeFiles/iio.dir/buffer.c.o @Parfait launched from the shell directly or also from RStudio, same result. [ 13%] Building C object CMakeFiles/iio.dir/buffer.c.o But i having problem with second command $ ./configure. checking for gcc option to accept ISO C89 none needed ERROR: configuration failed for package XML. * checking for gzopen in -lz. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. checking whether we are cross compiling no I wasn't see anyway to override this false positive libxml1 check, so a hack of a workaround you can use is to patch out that branch of the configure script. How to check for #1 being either `d` or `h` with latex3? /tmp/RtmpY66UhU/downloaded_packages DESeq2 . privacy statement. conda install -c r r-xml. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide, How did you launch the R shell above? Ubuntu and the circle of friends logo are trade marks of Canonical Limited and are used under licence. Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. of the following names: Add the installation prefix of "Python" to CMAKE_PREFIX_PATH or set That will install the build dependencies for the btrfs-tools version in your package repository, rather than for the newer version you're trying to build. -- Looking for newlocale - found R version 3.4.1 (2017-06-30) [ 8%] Building C object CMakeFiles/iio.dir/device.c.o To learn more, see our tips on writing great answers. BLAS: /home/kkarius/anaconda3/lib/R/lib/libRblas.so By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Here are my steps and the results. For me, this gives: Answers to some questions suggest adding the path to PKG_CONFIG_PATH. What does the power set mean in the construction of Von Neumann universe? Already on GitHub? Would you ever say "eat pig" instead of "eat pork"? Also you should know that pgModeler 0.9.2 is packaged in Ubuntu 20.04 LTS at https://packages.ubuntu.com/focal/pgmodeler, so it installable as simple as. -- Check for working C compiler: /usr/bin/cc -- works As brew tells you when it installs libxml2: This means that brew is not symlinking libxml2 to /usr/local/lib and /usr/local/include, and likely not linking the pkg-config file there as well, which is why libvisio can't find it. You can also subscribe without commenting. Upgrade Node.js to the latest version on Mac OS, Incompatible library version: nokogiri.bundle requires version 8.0.0 or later, but libiconv.2.dylib provides version 7.0.0, "code ." checking for xmlParseFile in -lxml2 yes https://github.com/analogdevicesinc/libiio.git, https://github.com/analogdevicesinc/libiio/blob/master/README.md. rev2023.4.21.43403. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Why in the Sierpiski Triangle is this set being used as the example for the OSC and not a more "natural"? "Signpost" puzzle from Tatham's collection. * Can you still use Commanders Strike if the only attack available to forego is an attack against an ally? Looking for job perks? Acoustic plug-in not working at home but works at Guitar Center, Short story about swapping bodies as a job; the person who hires the main character misuses his body. I've updated the README to explicitly mention this dependency. Could a subterranean river or aquifer generate enough continuous momentum to power a waterwheel for the purpose of producing electricity? I'm using autoconf 2.69. mkdir build When a gnoll vampire assumes its hyena form, do its HP change? installation of package XML had non-zero exit status, > sessionInfo() [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 To subscribe to this RSS feed, copy and paste this URL into your RSS reader. To my unluck, i ran into following errors: The quick solution to the above problem is you need to install libxml2-devel package. make all, [ 3%] Building C object CMakeFiles/iio.dir/backend.c.o [ 7%] Building C object CMakeFiles/iio.dir/channel.c.o this is the output if make all after cloning the repo and cmake ./: The text was updated successfully, but these errors were encountered: Well, did you install the development files of libxml2? /usr/include/libxml2/libxml/encoding.h:31:26: fatal error: unicode/ucnv.h: No such file or directory Problems install R XML package on CentOS 7, Traffic: 580 users visited in the last hour, https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz', https://cloud.r-project.org/src/contrib/XML_3.98-1.9.tar.gz, User Agreement and Privacy configure script cannot find libxml2 on mac. -- Performing Test WITH_NETWORK_EVENTFD - Success -- Looking for sys/types.h -- Check for working C compiler: /usr/bin/cc You can check what development packages are available for a particular library using the apt-cache search engine e.g. [ 30%] Building C object CMakeFiles/iio.dir/sort.c.o It only takes a minute to sign up. I'm hitting other issues now, will post a separate question if I can't work round these. Ah, so you're using Anaconda's R distribution. If you run: brew ls libxml2. checking for pkg-config /usr/bin/pkg-config The text was updated successfully, but these errors were encountered: The issue here isn't that you're missing xsltproc, but that you're missing the Autotools macro AX_PROG_XSLTPROC which looks for xsltproc. Have a question about this project? Site design / logo 2023 Stack Exchange Inc; user contributions licensed under CC BY-SA. -- Looking for in6addr_any - found On what basis are pardoning decisions made by presidents or governors when exercising their pardoning power? What does "up to" mean in "is first up to launch"? i am totally new about this so sorry if i am asking for such silly thing. Correct name of the libxml2 configuration file for pkg-config is libxml-2.0.pc, you have already installed it from libxml2-dev package. In your case, this is likely possible using: export PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/opt/libxml2/lib/pkgconfig" [2020-01-17 10:10 UTC] 823688826 at qq dot com -Status: Feedback +Status: [2020-01-17 10:10 UTC] 823688826 at qq dot com By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. R -q --vanilla < i have noticed that libxml-2.0.pc is exist in other directory i.e. What's the cheapest way to buy out a sibling's share of our parents house if I have no cash and want to pay less than the appraised value? I made sure xml2 and libxml2 are installed (via sudo apt-get install) but that's not enough. What is this brick with a round back and a stud on the side used for? Why does contour plot not show point(s) where function has a discontinuity? In order to get the libraries and header files necessary for compiling and building, there is usually a separate libXXX-dev package (-dev indicating that the packages are for development). I have libxml2 version 2.9.9-2 installed with cmake 3.15.4 on my Manjaro system. Can the game be left in an invalid state if all state-based actions are replaced? Ubuntu and the circle of friends logo are trade marks of Canonical Limited and are used under licence. The quick solution to the above problem is you need to install libxml2-devel package. -- Detecting C compile features - done Order relations on natural number objects in topoi, and symmetry. -- Looking for strerror_r - found @pcercuei correct me if I'm wrong here, but we don't really do anything special with libxml2 in cmake but rely on find_package. So the other option left was to install from source. The header files and library seem to be from /usr/include/libxml2/libxml/globals.h:18, -- Looking for sys/types.h - found Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). https://github.com/analogdevicesinc/libiio/blob/master/README.md. How can I control PNP and NPN transistors together from one pin? sudo apt-get install libxml2-dev I'm unable to determine which is the right version (libxml or libxml2) for 14.04 but you'll want to make sure you have the -dev version installed. Alternatively, you may set the environment variables LIBXML_CFLAGS and LIBXML_LIBS to avoid the need to call pkg-config. The problem is it's looking for libxml-2.0, not libxml2. [ 19%] Building C object CMakeFiles/iio.dir/scan.c.o [1] compiler_3.4.1 tools_3.4.1. // . libxml >>installed was1.8.3, did not work so I installed libxml2 2.2.2 >>and libxml2-devel 2.2.2. I have added all dependancy described there listed bellow: After adding dependancies i am trying to run bellow commands. I think there is a problem with the environment variables when you install R through conda. Minor 9, Patch 4 for 2.9.4 On whose turn does the fright from a terror dive end? I have nearly no idea about cmake, so I probably didn't find out everything, but the file that gets created with the include path seems very wrong: These paths should be /usr/inlucde/libxml2. Why don'y you use the conda package for CRAN's XML (called r-xml)? Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help Content Discovery initiative April 13 update: Related questions using a Review our technical responses for the 2023 Developer Survey, Error installing R 2.13.0 packages (caret) on Ubuntu 10.04, Unable to compile xps after installing ROOT, missing libraries, RCDK package installation fails in R studio. Connect and share knowledge within a single location that is structured and easy to search. Notify me of followup comments via e-mail. Content Discovery initiative April 13 update: Related questions using a Review our technical responses for the 2023 Developer Survey, Problems compiling libjingle/gtk+-2.0 for Mac OS X, XSP Configure fails due to mono module dependancy, Error libxml-2.0 not found when installing ggiraph, How to set path pygobject Macos catalina installing PyGTK, Having Trouble Downloading Tidyverse in R, "Signpost" puzzle from Tatham's collection. What is scrcpy OTG mode and how does it work? If you also run: ./configure --help. Interpreting non-statistically significant results: Do we have "no evidence" or "insufficient evidence" to reject the null? make: *** [all] Error 2. sorry for going dark on this one, I realized it was probably a problem with cmake or some other component. -- Looking for stdint.h Connect and share knowledge within a single location that is structured and easy to search. Why in the Sierpiski Triangle is this set being used as the example for the OSC and not a more "natural"? Refactoring has begun on some buffering and encoding code with the goal of checking whether we are cross compiling no directories. ^ So I'm not sure if this correct behaviour, since the libxml & libusb are both in the sysroot specified in the cmake line. Making statements based on opinion; back them up with references or personal experience. Have you tried doing the same command after rebooting your pc ? i have tried to install libxml2 with $ brew install libxml but its says Warning: libxml2-2.9.3 already installed. Already on GitHub? See the pkg-config man page for more details. I made sure xml2 and libxml2 are installed (via sudo apt-get install) but that's not enough. If total energies differ across different software, how do I decide which software to use? Embedded hyperlinks in a thesis or research paper. Interpreting non-statistically significant results: Do we have "no evidence" or "insufficient evidence" to reject the null? -- Performing Test HAS_WPEDANTIC checking for gcc option to accept ISO C89 none needed The pasted message is from Brew. How a top-ranked engineering school reimagined CS curriculum (Ep. Checking for 1.8: -I/home/kkarius/anaconda3/include/libxml2 -I/home/kkarius/anaconda3/include Can I connect multiple USB 2.0 females to a MEAN WELL 5V 10A power supply? USE_XML2 = yes All symbol information has been removed from the ELF version script to fix This release finally fixes symbol visibility on UNIX systems. Checking Irreducibility to a Polynomial with Non-constant Degree over Integer. rev2023.4.21.43403. I've corrected -libs to --libs (initial error from copying and pasting via MS Word). but setting the config in the R environment doesn't help: UPDATE I already had libxml2 installed in the system see: Make sure your system has the libxml-dev or libxml2-dev package installed. no configure: error: "libxml not found" ERROR: configuration failed for package 'XML' [ 22%] Building C object CMakeFiles/iio.dir/sort.c.o When I try to do an upgrade or install something, apt (-get or aptitude) throw an error, saying that perl can't find XML/SAX/Debian.pm while trying to configure libxml-libxml-perl. While these symbols were never declared in public I really don't get why it's not building on my systems, my workaround now is to set it to REQUIRED in the CMakeList.txt file, but I honestly have no idea what exactly that changes, it just works now. specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default What are the advantages of running a power tool on 240 V vs 120 V? Ask Ubuntu is a question and answer site for Ubuntu users and developers. -- Looking for stdint.h - found Sign up for a free GitHub account to open an issue and contact its maintainers and the community. If this is the same problem for you as it was for me, we should report the problem upstream to the XML maintainers. [ 15%] Building C object CMakeFiles/iio.dir/context.c.o By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. Like "libxml2-devel". * installing *source* package XML long story short: if "/bin" is in your PATH, cmake doesn't work correctly. checking for gcc gcc Make sure your system has the libxml-dev or libxml2-dev package installed. By clicking Sign up for GitHub, you agree to our terms of service and This doesn't work for me. I can build libiio using "make all", but then "make install" fails trying to write to /usr/lib even though I've specified my own sysroot in the cmake line. from /usr/include/libxml2/libxml/tree.h:1307, hi, when i configure dictconvert in dictconvert folder with ./configure command, then i get an error, it as follows: checking for libxml - version >= 2.5.0. no *** The xml2-config script installed by LIBXML could not be found *** If libxml was installed in PREFIX, make sure PREFIX/bin is in *** your path, or set the XML2_CONFIG environment variable to the *** full path to xml2-config. [ 25%] Building C object CMakeFiles/iio.dir/local.c.o Making statements based on opinion; back them up with references or personal experience. Generally to troubleshoot a configure problem, you should download the package tarball, run the installation, and inspect the config.log file. [OpenStack Glance]: Failed to contact the endpoint at https://localhost:9292 for discovery. How a top-ranked engineering school reimagined CS curriculum (Ep. As you can see, libxml2 is being found in /usr/lib and not in the sysroot defined. How do you know the names. -- Build files have been written to: /home/patricaholden/williamson/testbuild/Pro3-Linux/packages/libiio/build, Just to point out - we already provide binaries for armhf (Raspbian Stretch & Raspbian Jessie), they are linked from the readme at: To learn more, see our tips on writing great answers. It seems that R is picking up the libxml2 installation from Anaconda. I used sudo apt-get install libxml2-dev and it seemed to install ok. error: Don't move past current position; error: Limit number of parser errors; parser: Lower entity nesting limit with XML_PARSE_HUGE; parser: Don't increase depth twice when parsing internal entities; parser: Improve detection of entity loops; parser: Only report a single entity error; libxml.h: Remove dubious definition of LIBXML_STATIC Share Improve this answer Follow answered Mar 14, 2019 at 16:39 stdunbar 15.8k 10 35 50 Why xargs does not process the last argument? I note there is a pkg-config file listed for libxml2 by homebrew at: which is also available via a non-version-specific symlink as: so, if you have installed pkg-config with homebrew, like this: the solution may be just to add the path for that to your PKG_CONFIG_PATH with: Note: It is only after installing pkg-config (via brew) that homebrew will display pkg-config related "caveats" for many affected packages e.g. from /usr/include/libxml2/libxml/xmlmemory.h:218, LAPACK: /home/kkarius/anaconda3/lib/R/lib/libRlapack.so, locale: Thanks for contributing an answer to Stack Overflow! The error message suggested configure: error: "libxml not found", but. checking for sed /bin/sed By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. /usr/include/libxml2/libxml/encoding.h:31:26: fatal error: unicode/ucnv.h: No such file or directory simplifying this part of the code base and improving error reporting. Make sure it is in your PATH or set the PKG_CONFIG environment variable to the full path to pkg-config. ** package XML successfully unpacked and MD5 sums checked privacy statement. from /usr/include/libxml2/libxml/xmlmemory.h:218, libxml2-dev ERROR: configuration failed for package XML Thanks for trying omphalos! To reproduce your problem I installed Anaconda3 4.4.0 on RedHat 7.4, then: Use of this site constitutes acceptance of our User Agreement and Privacy No package 'libxml-2.0' found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. The output is this: > source("https://bioconductor.org/biocLite.R") Ask Ubuntu is a question and answer site for Ubuntu users and developers. mismatched. Using an Ohm Meter to test for bonding of a subpanel. checking for gcc gcc Unfortunately, through yum, i couldnt upgrade php! By not providing "FindPython.cmake" in CMAKE_MODULE_PATH this project has ~. [ 11%] Building C object CMakeFiles/iio.dir/device.c.o What positional accuracy (ie, arc seconds) is necessary to view Saturn, Uranus, beyond? SED_EXTENDED_ARG: -E What is scrcpy OTG mode and how does it work? Can you still use Commanders Strike if the only attack available to forego is an attack against an ally? One other thing, changing the PATH produces following error with CMake: CMake Warning at CMakeLists.txt:289 (message): -- Performing Test WITH_NETWORK_EVENTFD As you can see, libxml2 is being found in /usr/lib and not in the sysroot defined. > biocLite("XML") "Python_DIR" to a directory containing one of the above files. Realistically they should be interchangeable packages. checking for gzopen in -lz yes Did the drapes in old theatres actually say "ASBESTOS" on them? git clone https://github.com/analogdevicesinc/libiio.git To learn more, see our tips on writing great answers. Yet there seems to be a problem with libxml2. checking for sed /bin/sed Does a password policy with a restriction of repeated characters increase security? okay, I missed that I need to have it installed, now it works! Making statements based on opinion; back them up with references or personal experience. https://nick-black.com/bugzilla/show_bug.cgi?id=543 we had a bug on this uninformative error. It only takes a minute to sign up. Tikz: Numbering vertices of regular a-sided Polygon, Embedded hyperlinks in a thesis or research paper. What is this brick with a round back and a stud on the side used for? As the error message indicates, you need to specify the libxml2 path using PKG_CONFIG_PATH. 2. Making 'packages.html' done Because configure it self is autogenerated from configure.ac using autotools, Making statements based on opinion; back them up with references or personal experience. Alternatively, you may set the environment variables LIBXML_CFLAGS and LIBXML_LIBS to avoid the need to call pkg-config. configure: error: "libxml not found" Asking for help, clarification, or responding to other answers. Ubuntu 14.04 configure: error: "libxml not found". In file included from /usr/include/libxml2/libxml/parser.h:810:0, To subscribe to this RSS feed, copy and paste this URL into your RSS reader. R itself was installed using anaconda. trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz' -- Looking for pthread_setname_np Why does contour plot not show point(s) where function has a discontinuity? Understanding the probability of measurement w.r.t. What are the advantages of running a power tool on 240 V vs 120 V? By clicking Sign up for GitHub, you agree to our terms of service and compilation terminated. English version of Russian proverb "The hedgehogs got pricked, cried, but continued to eat the cactus", How to convert a sequence of integers into a monomial. How to automatically extend windows virtual disk size [Openstack], No such file or directory c++ Error [CentOS], How to configure Open vSwitch bridge for OpenStack, Too many connections for neutron-db-manage [MySQL], How to manually install higher version of PIP for Python v2.7, [CentOS 7]: Yum install python-pip | No package python-pip available, [OpenStack noVNC]: Code 400, message Client must support binary or base64 protocol [Solved], [CentOS Stream 8]: Error: Unknown repo epel [Solved]. [1] BiocInstaller_1.26.1, loaded via a namespace (and not attached): Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide, for libxml++2.6 sudo apt-get install libxml++2.6-dev.
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