* installing *source* package 'ribiosUtils' ...
** package 'ribiosUtils' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2026_02_04_01_50_01_15123/RtmpApz3yJ/R.INSTALL1038860673303/ribiosUtils/src'
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c affyfileHandler.c -o affyfileHandler.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c algutil.c -o algutil.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alphatrans.c -o alphatrans.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c arg.c -o arg.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c array.c -o array.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c avlTree.c -o avlTree.o
In function 'avl_nodeAssignChildren',
inlined from 'avl_nodeRestructure' at avlTree.c:307:3:
avlTree.c:179:6: warning: 'arrNodes[0]' may be used uninitialized [-Wmaybe-uninitialized]
179 | if (leftChild != NULL)
| ^
avlTree.c: In function 'avl_nodeRestructure':
avlTree.c:249:11: note: 'arrNodes[0]' was declared here
249 | AvlNode arrNodes[7];
| ^~~~~~~~
In function 'avl_nodeAssignChildren',
inlined from 'avl_nodeRestructure' at avlTree.c:307:3:
avlTree.c:178:20: warning: 'arrNodes[1]' may be used uninitialized [-Wmaybe-uninitialized]
178 | parent->leftNode = leftChild;
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~
avlTree.c: In function 'avl_nodeRestructure':
avlTree.c:249:11: note: 'arrNodes[1]' was declared here
249 | AvlNode arrNodes[7];
| ^~~~~~~~
In function 'avl_nodeAssignChildren',
inlined from 'avl_nodeRestructure' at avlTree.c:307:3:
avlTree.c:182:6: warning: 'arrNodes[2]' may be used uninitialized [-Wmaybe-uninitialized]
182 | if (rightChild != NULL)
| ^
avlTree.c: In function 'avl_nodeRestructure':
avlTree.c:249:11: note: 'arrNodes[2]' was declared here
249 | AvlNode arrNodes[7];
| ^~~~~~~~
avlTree.c:306:27: warning: 'arrNodes[3]' may be used uninitialized [-Wmaybe-uninitialized]
306 | arrNodes[3]->parentNode = unBalNode->parentNode;
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
avlTree.c:249:11: note: 'arrNodes[3]' was declared here
249 | AvlNode arrNodes[7];
| ^~~~~~~~
In function 'avl_nodeAssignChildren',
inlined from 'avl_nodeRestructure' at avlTree.c:308:3:
avlTree.c:179:6: warning: 'arrNodes[4]' may be used uninitialized [-Wmaybe-uninitialized]
179 | if (leftChild != NULL)
| ^
avlTree.c: In function 'avl_nodeRestructure':
avlTree.c:249:11: note: 'arrNodes[4]' was declared here
249 | AvlNode arrNodes[7];
| ^~~~~~~~
In function 'avl_nodeAssignChildren',
inlined from 'avl_nodeRestructure' at avlTree.c:308:3:
avlTree.c:178:20: warning: 'arrNodes[5]' may be used uninitialized [-Wmaybe-uninitialized]
178 | parent->leftNode = leftChild;
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~
avlTree.c: In function 'avl_nodeRestructure':
avlTree.c:249:11: note: 'arrNodes[5]' was declared here
249 | AvlNode arrNodes[7];
| ^~~~~~~~
In function 'avl_nodeAssignChildren',
inlined from 'avl_nodeRestructure' at avlTree.c:308:3:
avlTree.c:182:6: warning: 'arrNodes[6]' may be used uninitialized [-Wmaybe-uninitialized]
182 | if (rightChild != NULL)
| ^
avlTree.c: In function 'avl_nodeRestructure':
avlTree.c:249:11: note: 'arrNodes[6]' was declared here
249 | AvlNode arrNodes[7];
| ^~~~~~~~
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c binalgparser.c -o binalgparser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bitmap.c -o bitmap.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c biurl.c -o biurl.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c blastdb.c -o blastdb.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c blastparser.c -o blastparser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c chemutil.c -o chemutil.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c combi.c -o combi.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c eval.c -o eval.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c forest.c -o forest.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c format.c -o format.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fuzzparser.c -o fuzzparser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c geometry.c -o geometry.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c graphalgo.c -o graphalgo.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c graphics.c -o graphics.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hash.c -o hash.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hierclus.c -o hierclus.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hlrmisc.c -o hlrmisc.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hmmparser.c -o hmmparser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c html.c -o html.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c htmlform.c -o htmlform.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c linestream.c -o linestream.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lnk.c -o lnk.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c log.c -o log.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matvec.c -o matvec.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c msfparser.c -o msfparser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pagedesign.c -o pagedesign.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c patternmatch.c -o patternmatch.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pearsonfastaparser.c -o pearsonfastaparser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c phraplightparser.c -o phraplightparser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c plabla.c -o plabla.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c primer3parser.c -o primer3parser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c properties.c -o properties.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwdecode.c -o pwdecode.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_endec.c -o r_endec.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_mmatch.c -o r_mmatch.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_trim.c -o r_trim.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rdbu.c -o rdbu.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c recipes.c -o recipes.o
recipes.c: In function 'rcp_svdcmp':
recipes.c:1408:21: warning: 'nm' may be used uninitialized [-Wmaybe-uninitialized]
1408 | y = a[j][nm];
| ^
recipes.c:1275:10: note: 'nm' was declared here
1275 | int jj,nm;
| ^~
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seqautil.c -o seqautil.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequenceAlignment.c -o sequenceAlignment.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sequtil.c -o sequtil.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c statistics.c -o statistics.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c stringlist.c -o stringlist.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c wiseparser.c -o wiseparser.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c wwwsession.c -o wwwsession.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xmlbuilder.c -o xmlbuilder.o
gcc -I"D:/RCompile/recent/R-4.4.3/include" -DNDEBUG -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -I../inst/include -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c xmlparser.c -o xmlparser.o
gcc -shared -s -static-libgcc -o ribiosUtils.dll tmp.def affyfileHandler.o algutil.o alphatrans.o arg.o array.o avlTree.o binalgparser.o bitmap.o biurl.o blastdb.o blastparser.o chemutil.o combi.o eval.o forest.o format.o fuzzparser.o geometry.o graphalgo.o graphics.o hash.o hierclus.o hlrmisc.o hmmparser.o html.o htmlform.o init.o linestream.o lnk.o log.o matvec.o msfparser.o pagedesign.o patternmatch.o pearsonfastaparser.o phraplightparser.o plabla.o primer3parser.o properties.o pwdecode.o r_endec.o r_mmatch.o r_trim.o rdbu.o recipes.o seqautil.o sequenceAlignment.o sequtil.o statistics.o stringlist.o wiseparser.o wwwsession.o xmlbuilder.o xmlparser.o -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2026_02_04_01_50_01_15123/RtmpApz3yJ/R.INSTALL1038860673303/ribiosUtils/src'
make[1]: Entering directory '/d/temp/2026_02_04_01_50_01_15123/RtmpApz3yJ/R.INSTALL1038860673303/ribiosUtils/src'
make[1]: Leaving directory '/d/temp/2026_02_04_01_50_01_15123/RtmpApz3yJ/R.INSTALL1038860673303/ribiosUtils/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-ribiosUtils/00new/ribiosUtils/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'ribiosUtils' as ribiosUtils_1.7.7.zip
* DONE (ribiosUtils)