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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL flowClust
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* 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... gawk
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 <config-patches@gnu.org> in order to provide the needed
information to handle your system.
config.guess timestamp = 2007-05-17
uname -m = aarch64
uname -r = 5.15.0-58-generic
uname -s = Linux
uname -v = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023
/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 = 5.15.0-58-generic
UNAME_SYSTEM = Linux
UNAME_VERSION = #64-Ubuntu SMP Thu Jan 5 12:06:43 UTC 2023
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 '/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include': No such file or directory
configure: Using the following compilation and linking flags for flowClust
configure: PKG_CFLAGS= -I/home/biocbuild/bbs-3.17-bioc/meat/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
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC -g -O2 -Wall -c BoxCox.c -o BoxCox.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC -g -O2 -Wall -c BoxCoxPriors.c -o BoxCoxPriors.o
BoxCoxPriors.c: In function ‘BoxCoxGradientPriors’:
BoxCoxPriors.c:57:23: warning: unused variable ‘rowZ’ [-Wunused-variable]
57 | rowPrecision, rowZ, rowLambda0;
| ^~~~
BoxCoxPriors.c:33:31: warning: unused variable ‘kappa0’ [-Wunused-variable]
33 | double *nu0 = p->nu0, kappa0 = p->kappa0;
| ^~~~~~
BoxCoxPriors.c:32:14: warning: unused variable ‘itersolve’ [-Wunused-variable]
32 | int *itersolve = p->itersolve;
| ^~~~~~~~~
BoxCoxPriors.c:31:13: warning: unused variable ‘iter’ [-Wunused-variable]
31 | int iter = p->iter;
| ^~~~
BoxCoxPriors.c:28:13: warning: unused variable ‘model’ [-Wunused-variable]
28 | int model = *p->model;
| ^~~~~
BoxCoxPriors.c:23:21: warning: unused variable ‘SumZlogY’ [-Wunused-variable]
23 | gsl_vector *SumZlogY = p->SumZlogY;
| ^~~~~~~~
BoxCoxPriors.c:15:21: warning: unused variable ‘Precision’ [-Wunused-variable]
15 | gsl_matrix *Precision = p->Precision; // will be updated
| ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC -g -O2 -Wall -c Nu.c -o Nu.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC -g -O2 -Wall -c flowClust.c -o flowClust.o
flowClust.c: In function ‘flowClust’:
flowClust.c:48:9: warning: unused variable ‘matrixZUY2’ [-Wunused-variable]
48 | matrixZUY2;
| ^~~~~~~~~~
flowClust.c:46:55: warning: unused variable ‘subRowZUY2’ [-Wunused-variable]
46 | rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
| ^~~~~~~~~~
flowClust.c:46:46: warning: unused variable ‘rowZUY2’ [-Wunused-variable]
46 | rowYTransS, rowZUY, subRowZUY, rowZ, rowZUY2, subRowZUY2;
| ^~~~~~~
flowClust.c: In function ‘ECMUpdateSigmaG2’:
flowClust.c:1111:13: warning: unused variable ‘i’ [-Wunused-variable]
1111 | int i=0;
| ^
At top level:
flowClust.c:10:27: warning: ‘CEntries’ defined but not used [-Wunused-const-variable=]
10 | static const R_CMethodDef CEntries[] = { { "flowClust", (DL_FUNC) & flowClust,
| ^~~~~~~~
flowClust.c: In function ‘flowClust’:
flowClust.c:702:34: warning: ‘s3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
702 | status = gsl_min_fminimizer_set(s3, &F3, *nu, *nuLow, *nuUp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:647:57: warning: ‘s2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
647 | nu_hi = gsl_root_fsolver_x_upper(s2);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
flowClust.c:348:56: warning: ‘s’ may be used uninitialized in this function [-Wmaybe-uninitialized]
348 | x_hi = gsl_root_fsolver_x_upper(s);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC -g -O2 -Wall -c flowClustGaussian.c -o flowClustGaussian.o
flowClustGaussian.c: In function ‘flowClustGaussian’:
flowClustGaussian.c:207:56: warning: ‘s’ may be used uninitialized in this function [-Wmaybe-uninitialized]
207 | x_hi = gsl_root_fsolver_x_upper(s);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/meat/flowClust/src/gslbuild/include -DGSL_MAJOR=1 -DGSL_MINOR=13 -DGSL_STATIC -fPIC -g -O2 -Wall -c ranMVNT.c -o ranMVNT.o
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o flowClust.so BoxCox.o BoxCoxPriors.o Nu.o flowClust.o flowClustGaussian.o ranMVNT.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/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, DLLpath = DLLpath, ...):
unable to load shared object '/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-flowClust/00new/flowClust/libs/flowClust.so':
/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-flowClust/00new/flowClust/libs/flowClust.so: undefined symbol: gsl_min_fminimizer_brent
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/flowClust’
Yikun
commented
1 year ago