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Can't seem to install on raspian bullseye #21

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arnaudcol opened this issue Sep 15, 2022 · 0 comments
Open

Can't seem to install on raspian bullseye #21

arnaudcol opened this issue Sep 15, 2022 · 0 comments

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@arnaudcol
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The package seems to compile correctly but it doesn't complete the installation. Log is pasted below

  • installing source package ‘flowClust’ ...
    ** using staged installation
    configure: Using bundled GSL.
    configure: Searching for the compilers specified by R.
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking how to run the C preprocessor... gcc -E
    untarring gsl...
    configure: Preparing to compile GSL.
    configure: Configuring bundled GSL.
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
    checking for gawk... no
    checking for mawk... mawk
    checking whether make sets $(MAKE)... yes
    checking whether to enable maintainer-specific portions of Makefiles... no
    checking whether make sets $(MAKE)... (cached) yes
    checking build system type... ./config.guess: unable to guess system type

This script, last modified 2007-05-17, 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://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
and
http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub

If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to [email protected] in order to provide the needed
information to handle your system.

config.guess timestamp = 2007-05-17

uname -m = aarch64
uname -r = 5.15.61-v8+
uname -s = Linux
uname -v = #1579 SMP PREEMPT Fri Aug 26 11:16:44 BST 2022

/usr/bin/uname -p = unknown
/bin/uname -X =

hostinfo =
/bin/universe =
/usr/bin/arch -k =
/bin/arch = aarch64
/usr/bin/oslevel =
/usr/convex/getsysinfo =

UNAME_MACHINE = aarch64
UNAME_RELEASE = 5.15.61-v8+
UNAME_SYSTEM = Linux
UNAME_VERSION = #1579 SMP PREEMPT Fri Aug 26 11:16:44 BST 2022
configure: error: cannot guess build type; you must specify one
cp: will not overwrite just-created 'gsl/test.h' with 'roots/test.h'
cp: will not overwrite just-created 'gsl/error.h' with 'specfunc/error.h'
cp: will not overwrite just-created 'gsl/view.h' with 'vector/view.h'
make: *** No rule to make target 'install'. Stop.
cp: cannot create directory '/tmp/RtmpgXA9fs/R.INSTALL346587b0d8e1e/flowClust/sr c/gslbuild/include': No such file or directory
configure: Using the following compilation and linking flags for flowClust
configure: PKG_CFLAGS= -I/tmp/RtmpgXA9fs/R.INSTALL346587b0d8e1e/flowClust/src /gslbuild/include
configure: PKG_LIBS=
configure: FLOWCLUST_DEFS=-DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC
configure: Compiling using GSL version: '1.13.0'.
configure: Using bundled GSL: 'yes'.
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/opt/R/release/lib/R/include" -DNDEBUG -I/usr/local/include -I/tmp/Rtm pgXA9fs/R.INSTALL346587b0d8e1e/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGS L_MINOR=13 -DGSL_STATIC -fpic -g -O2 -c BoxCox.c -o BoxCox.o
gcc -I"/opt/R/release/lib/R/include" -DNDEBUG -I/usr/local/include -I/tmp/Rtm pgXA9fs/R.INSTALL346587b0d8e1e/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGS L_MINOR=13 -DGSL_STATIC -fpic -g -O2 -c BoxCoxPriors.c -o BoxCoxPriors.o
gcc -I"/opt/R/release/lib/R/include" -DNDEBUG -I/usr/local/include -I/tmp/Rtm pgXA9fs/R.INSTALL346587b0d8e1e/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGS L_MINOR=13 -DGSL_STATIC -fpic -g -O2 -c Nu.c -o Nu.o
gcc -I"/opt/R/release/lib/R/include" -DNDEBUG -I/usr/local/include -I/tmp/Rtm pgXA9fs/R.INSTALL346587b0d8e1e/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGS L_MINOR=13 -DGSL_STATIC -fpic -g -O2 -c flowClust.c -o flowClust.o
gcc -I"/opt/R/release/lib/R/include" -DNDEBUG -I/usr/local/include -I/tmp/Rtm pgXA9fs/R.INSTALL346587b0d8e1e/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGS L_MINOR=13 -DGSL_STATIC -fpic -g -O2 -c flowClustGaussian.c -o flowClustGaussi an.o
gcc -I"/opt/R/release/lib/R/include" -DNDEBUG -I/usr/local/include -I/tmp/Rtm pgXA9fs/R.INSTALL346587b0d8e1e/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGS L_MINOR=13 -DGSL_STATIC -fpic -g -O2 -c ranMVNT.c -o ranMVNT.o
gcc -shared -L/opt/R/release/lib/R/lib -L/usr/local/lib -o flowClust.so BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L/opt/R/release/ lib/R/lib -lR
installing to /opt/R/release/lib/R/library/00LOCK-flowClust/00new/flowClust/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘Map’ in package ‘flowClust’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘flowClust’ in dyn.load(file, DLLpat h = DLLpath, ...):
unable to load shared object '/opt/R/release/lib/R/library/00LOCK-flowClust/00n ew/flowClust/libs/flowClust.so':
/opt/R/release/lib/R/library/00LOCK-flowClust/00new/flowClust/libs/flowClust.s o: undefined symbol: gsl_min_fminimizer_brent
Error: loading failed
Execution halted
ERROR: loading failed

  • removing ‘/opt/R/release/lib/R/library/flowClust’

Any suggestions?

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