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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
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.
The package seems to compile correctly but it doesn't complete the installation. Log is pasted below
** 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
Any suggestions?
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