* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘seqinr’ ...
** package ‘seqinr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/Rtmpq8yfI1/R.INSTALL2bfb3d2c2dfe24/seqinr/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c alignment.c -o alignment.o
alignment.c: In function ‘read_phylip_align’:
alignment.c:614:14: warning: ‘*<unknown>’ may be used uninitialized [-Wmaybe-uninitialized]
614 | l = q - seq[totseqs - 1];
| ~~~^~~~~~~~~~~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fastacc.c -o fastacc.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c getzlibsock.c -o getzlibsock.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c kaks.c -o kaks.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c packagename_init.c -o packagename_init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c zsockr.c -o zsockr.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o seqinr.so alignment.o fastacc.o getzlibsock.o kaks.o packagename_init.o util.o zsockr.o -lz -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmpq8yfI1/R.INSTALL2bfb3d2c2dfe24/seqinr/src'
make[1]: Entering directory '/tmp/Rtmpq8yfI1/R.INSTALL2bfb3d2c2dfe24/seqinr/src'
make[1]: Leaving directory '/tmp/Rtmpq8yfI1/R.INSTALL2bfb3d2c2dfe24/seqinr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-seqinr/00new/seqinr/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘seqinr’
finding HTML links ... done
AAstat html
AnoukResult html
ECH html
EXP html
GC html
JLO html
SEQINR.UTIL html
SeqAcnucWeb html
SeqFastaAA html
SeqFastadna html
SeqFrag html
a html
aaa html
aacost html
aaindex html
acnucopen html
al2bp html
alllistranks html
amb html
as.alignment html
as.matrix.alignment html
autosocket html
baselineabif html
bma html
c2s html
cai html
caitab html
chargaff html
choosebank html
circle html
closebank html
clustal html
col2alpha html
comp html
computePI html
consensus html
count html
countfreelists html
countsubseqs html
crelistfromclientdata html
dia.bactgensize html
dinucl html
dist.alignment html
dotPlot html
dotchart.uco html
draw.oriloc html
draw.rearranged.oriloc html
draw.recstat html
ec999 html
extract.breakpoints html
extractseqs html
fasta html
fastacc html
gb2fasta html
gbk2g2 html
gbk2g2.euk html
gcO2 html
gcT html
get.db.growth html
getAnnot html
getFrag html
getKeyword html
getLength html
getLocation html
getName html
getSequence html
getTrans html
getType html
getlistrank html
getliststate html
gfrag html
ghelp html
gs500liz html
identifiler html
isenum html
kaks-torture html
kaks html
knowndbs html
lseqinr html
m16j html
mase html
modifylist html
move html
msf html
n2s html
oriloc html
pK html
parser.socket html
peakabif html
permutation html
phylip html
plot.SeqAcnucWeb html
plotPanels html
plotabif html
plotladder html
pmw html
prepgatannots html
prettyseq html
print.SeqAcnucWeb html
print.qaw html
prochlo html
query html
read.abif html
read.alignment html
read.fasta html
readBins html
readPanels html
readfirstrec html
readsmj html
rearranged.oriloc html
recstat html
residuecount html
revaligntest html
reverse.align html
rot13 html
s2c html
s2n html
savelist html
seqinr-package html
setlistname html
splitseq html
stresc html
stutterabif html
swap html
syncodons html
synsequence html
tablecode html
test.co.recstat html
test.li.recstat html
toyaa html
toycodon html
translate html
trimSpace html
uco html
ucoweight html
waterabs html
where.is.this.acc html
words html
words.pos html
write.fasta html
zscore html
*** copying figures
** building package indices
** 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 (seqinr)