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gvds
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@gvds-23478
Last seen 3.9 years ago
Installing Rgraphviz in R ver. 4.0 & Bioconductor ver. 3.11.1 on Kubuntu 20.04 fails with the following error.
In file included from LL_funcs.c:1:
common.h:16:10: fatal error: gvc.h: No such file or directory
16 | #include <gvc.h>
| ^~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:167: LL_funcs.o] Error 1
ERROR: compilation failed for package ‘Rgraphviz’
.
sessionInfo output:
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_ZA.UTF-8 LC_NUMERIC=C LC_TIME=en_ZA.UTF-8 LC_COLLATE=en_ZA.UTF-8 LC_MONETARY=en_ZA.UTF-8 LC_MESSAGES=en_ZA.UTF-8
[7] LC_PAPER=en_ZA.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_ZA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] rstudioapi_0.11 magrittr_1.5 usethis_1.6.1 devtools_2.3.0 pkgload_1.0.2 R6_2.4.1 rlang_0.4.5 fansi_0.4.1 tools_4.0.0 pkgbuild_1.0.7
[11] packrat_0.5.0 sessioninfo_1.1.1 cli_2.0.2 withr_2.2.0 ellipsis_0.3.0 remotes_2.1.1 assertthat_0.2.1 digest_0.6.25 rprojroot_1.3-2 crayon_1.3.4
[21] processx_3.4.2 callr_3.4.3 fs_1.4.1 ps_1.3.2 curl_4.3 testthat_2.3.2 memoise_1.1.0 glue_1.4.0 compiler_4.0.0 desc_1.2.0
[31] backports_1.1.6 prettyunits_1.1.1
How are you installing Rgraphviz? You should not be using an external Graphviz by default, so I am surprised by this error. You can send me the entire installation output.
Best, Kasper
Hi! I know it has been a long time this thread was first created but I am currently making a Docker Container for an app and am running into the same issue as the OP. I am using an Ubuntu:latest base image and have installed the base R in addition to being able to install other Bioconductor packages. I am not quite sure how to approach this issue and I apologize if I am missing something trivial.
Here is my output. I greatly appreciate your help!
This script, last modified 2009-11-20, has failed to recognize the operating system you are using. It is advised that you download the most up to date version of the config scripts from
http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD and http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
If the version you run (config/config.guess) is already up to date, please send the following data and any information you think might be pertinent to config-patches@gnu.org in order to provide the needed information to handle your system.
config.guess timestamp = 2009-11-20
uname -m = aarch64 uname -r = 5.15.49-linuxkit uname -s = Linux uname -v = #1 SMP PREEMPT Tue Sep 13 07:51:32 UTC 2022
/usr/bin/uname -p = aarch64 /bin/uname -X =
hostinfo = /bin/universe = /usr/bin/arch -k = /bin/arch = aarch64 /usr/bin/oslevel = /usr/convex/getsysinfo =
UNAME_MACHINE = aarch64 UNAME_RELEASE = 5.15.49-linuxkit UNAME_SYSTEM = Linux UNAME_VERSION = #1 SMP PREEMPT Tue Sep 13 07:51:32 UTC 2022 configure: error: cannot guess build type; you must specify one make: No rule to make target 'install'. Stop. cp: cannot stat '/tmp/RtmpfsjcJB/R.INSTALL1929b87a/Rgraphviz/src/libunix/lib/': No such file or directory cp: cannot stat '/tmp/RtmpfsjcJB/R.INSTALL1929b87a/Rgraphviz/src/libunix/lib/graphviz/*': No such file or directory checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for deflateBound in -lz... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for whether compiler has bool... yes configure: Using the following compilation and linking flags for Rgraphviz configure: PKG_CFLAGS= -I/tmp/RtmpfsjcJB/R.INSTALL1929b87a/Rgraphviz/src/libunix/include/graphviz configure: PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz configure: GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 configure: Compiling using Graphviz version: '2.28.0'. configure: Using bundled Graphviz: 'TRUE'. configure: creating ./config.status config.status: creating R/graphviz_build_version.R config.status: creating src/Makevars libs gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpfsjcJB/R.INSTALL1929b87a/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -ffile-prefix-map=/build/r-base-nNSpe3/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c LL_funcs.c -o LL_funcs.o In file included from LL_funcs.c:1: common.h:16:10: fatal error: gvc.h: No such file or directory 16 | #include <gvc.h> | ^
~~ compilation terminated. make: *** [/usr/lib/R/etc/Makeconf:168: LL_funcs.o] Error 1 ERROR: compilation failed for package 'Rgraphviz'The downloaded source packages are in '/tmp/Rtmpxr1wTr/downloaded_packages' Warning message: In install.packages(...) : installation of package 'Rgraphviz' had non-zero exit status