* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘NMF’ ...
** package ‘NMF’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpkQFG5b/R.INSTALL32e28c73b27035/NMF/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distance.cpp -o distance.o
distance.cpp: In function ‘SEXPREC* Euclidean_rss(SEXP, SEXP)’:
distance.cpp:43:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
43 | if( INTEGER(GET_DIM(y))[1] != p )
| ^~
distance.cpp:46:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
46 | if( TYPEOF(x) == REALSXP ){// x is double
| ^~
distance.cpp: In function ‘SEXPREC* KL_divergence(SEXP, SEXP)’:
distance.cpp:69:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
69 | if( INTEGER(GET_DIM(y))[1] != p )
| ^~
distance.cpp:72:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
72 | if( TYPEOF(x) == REALSXP ){// x is double
| ^~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c divergence.cpp -o divergence.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c euclidean.cpp -o euclidean.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o NMF.so distance.o divergence.o euclidean.o registerDynamicSymbol.o utils.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpkQFG5b/R.INSTALL32e28c73b27035/NMF/src'
make[1]: Entering directory '/tmp/RtmpkQFG5b/R.INSTALL32e28c73b27035/NMF/src'
make[1]: Leaving directory '/tmp/RtmpkQFG5b/R.INSTALL32e28c73b27035/NMF/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-NMF/00new/NMF/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Setting package specific options: package:NMF:logger (1 default option(s))
Setting package specific options: package:NMF (10 default option(s))
Creating a generic function for ‘plot’ from ‘graphics’ in package ‘NMF’
(from the saved implicit definition)
Creating meta registry in package 'NMF' ... OK
Creating registry 'extra_handler' in package 'NMF' ... OK
Creating registry 'extra_action' in package 'NMF' ... OK
Registering extra handler 'install.packages' [function] ... OK
Creating registry 'algorithm' in package 'NMF' ... OK
Registering NMF algorithm '.R#brunet' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'brunet' [NMFStrategyIterative] based on template '.R#brunet' ... OK
Registering NMF algorithm 'KL' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.R#lee' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'lee' [NMFStrategyIterative] based on template '.R#lee' ... OK
Registering NMF algorithm 'Frobenius' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.R#offset' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'offset' [NMFStrategyIterative] based on template '.R#offset' ... OK
Registering NMF algorithm '.R#nsNMF' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'nsNMF' [NMFStrategyIterative] based on template '.R#nsNMF' ... OK
Registering NMF algorithm 'ls-nmf' [NMFStrategyIterative] ... OK
Registering NMF algorithm 'pe-nmf' [NMFStrategyIterative] ... OK
Registering NMF algorithm '.siNMF' [NMFStrategyIterative] based on template 'lee' ... OK
Registering NMF algorithm 'siNMF' [NMFStrategyIterative] based on template 'lee' ... OK
Registering NMF algorithm 'snmf/r' [NMFStrategyFunction] ... OK
Registering NMF algorithm 'snmf/l' [NMFStrategyFunction] ... OK
Registering extra action 'bigmemory' for handler 'install.packages' ... OK
Registering extra action 'synchronicity' for handler 'install.packages' ... OK
Creating registry 'seed' in package 'NMF' ... OK
Registering NMF seeding method 'none' [NMFSeed] ... OK
Registering NMF seeding method 'random' [NMFSeed] ... OK
Registering NMF seeding method 'ica' [NMFSeed] ... OK
Registering NMF seeding method 'nndsvd' [NMFSeed] ... OK
** help
*** installing help indices
converting help for package ‘NMF’
finding HTML links ... done
Frobenius-nmf html
KL-nmf html
NMF-class html
NMF-defunct html
NMF-deprecated html
NMF-package html
NMFList-class html
NMFOffset-class html
NMFSeed-class html
NMFStrategy-class html
NMFStrategy html
NMFStrategyFunction-class html
NMFStrategyIterative-class html
NMFfit-class html
finding level-2 HTML links ... done
NMFfitX-class html
NMFfitX html
NMFfitX1-class html
NMFfitXn-class html
NMFns-class html
NMFstd-class html
RNG html
SNMF-nmf html
Strategy-class html
advanced html
aggregate.measure html
aheatmap html
algorithm-commaNMFList-method html
algorithmic html
assess html
atrack html
basis-coef-methods html
basiscor html
bioc html
c-commaNMF-method html
canFit html
ccBreaks html
ccPalette html
ccRamp html
ccSpec html
checkErrors html
cluster_mat html
connectivity html
consensus-commaNMFfitX1-method html
consensus-commaNMFfitXn-method html
consensushc html
cophcor html
cutdendro html
deviance html
dimnames html
dims html
dispersion html
dot-fcnnls html
esGolub html
fcnnls html
fit html
fitted html
foreach html
gfile html
grid html
heatmaps html
inplace html
isCRANcheck html
latex html
lsNMF-nmf html
lverbose html
match_atrack html
nmf-compare html
nmf html
nmf.equal html
nmfAlgorithm html
nmfApply html
nmfCheck html
nmfEstimateRank html
nmfFormals html
nmfModel html
nmfObject html
nmfReport html
nmfSeed html
nmfWrapper html
nmf_update_KL html
nmf_update_euclidean html
nneg html
nsNMF-nmf html
objective-commaNMFfit-method html
offset-commaNMFOffset-method html
offset-commaNMFfit-method html
offset-nmf html
options html
parallel html
parse_formula html
plot-commaNMFfit-commamissing-method html
predict html
profplot html
purity html
randomize html
registry-algorithm html
residuals html
revPalette html
rmatrix html
rnmf html
rss html
runtime-commaNMFList-method html
runtime.all-commaNMFfitXn-method html
scale.NMF html
scores html
seed html
setNMFMethod html
setNMFSeed html
setup html
show-commaNMF-method html
show-commaNMFList-method html
show-commaNMFOffset-method html
show-commaNMFSeed-method html
show-commaNMFStrategyIterative-method html
show-commaNMFfit-method html
show-commaNMFfitX-method html
show-commaNMFfitX1-method html
show-commaNMFfitXn-method html
show-commaNMFns-method html
silhouette.NMF html
smoothing html
sparseness html
staticVar html
stop-NMF html
subset-NMF html
syntheticNMF html
t.NMF html
terms-internal html
terms html
txtProgressBar html
types html
utils html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NMF)