downloading reverse dependencies ... downloading RobLoxBioC_1.2.2.tar.gz ... ok downloading ROptEst_1.3.5.tar.gz ... ok installing dependencies ‘affydata’, ‘beadarray’, ‘beadarrayExampleData’, ‘distrMod’, ‘hgu95av2cdf’, ‘illuminaHumanv3.db’, ‘RandVar’, ‘RobAStBase’, ‘RobLox’ also installing the dependencies ‘base64’, ‘BeadDataPackR’, ‘illuminaio’ begin installing package ‘base64’ begin installing package ‘BeadDataPackR’ begin installing package ‘RandVar’ begin installing package ‘affydata’ begin installing package ‘hgu95av2cdf’ begin installing package ‘illuminaHumanv3.db’ * installing *source* package ‘base64’ ... ** this is package ‘base64’ version ‘2.0.2’ ** package ‘base64’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 * DONE (base64) begin installing package ‘illuminaio’ * installing *source* package ‘BeadDataPackR’ ... ** this is package ‘BeadDataPackR’ version ‘1.58.0’ ** package ‘BeadDataPackR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9aU3fz/R.INSTALL27fedc31a0432a/BeadDataPackR/src' gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c BeadDataPackR.c -o BeadDataPackR.o gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_BeadDataPackR.c -o R_init_BeadDataPackR.o gcc-14 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o BeadDataPackR.so BeadDataPackR.o R_init_BeadDataPackR.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9aU3fz/R.INSTALL27fedc31a0432a/BeadDataPackR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BeadDataPackR/00new/BeadDataPackR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (BeadDataPackR) * installing *source* package ‘illuminaio’ ... ** this is package ‘illuminaio’ version ‘0.48.0’ ** package ‘illuminaio’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpTEyVuh/R.INSTALL27ff4e1da5d03e/illuminaio/src' gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c 000.init.c -o 000.init.o gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c des.c -o des.o gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c local_des.c -o local_des.o gcc-14 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o illuminaio.so 000.init.o des.o local_des.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpTEyVuh/R.INSTALL27ff4e1da5d03e/illuminaio/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-illuminaio/00new/illuminaio/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (illuminaio) begin installing package ‘beadarray’ * installing *source* package ‘affydata’ ... ** this is package ‘affydata’ version ‘1.54.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Package LibPath [1,] "affydata" "/home/hornik/tmp/CRAN_recheck/Library/00LOCK-affydata/00new" Item Title [1,] "Dilution" "AffyBatch instance Dilution" ** testing if installed package can be loaded from final location Package LibPath Item [1,] "affydata" "/home/hornik/tmp/CRAN_recheck/Library" "Dilution" Title [1,] "AffyBatch instance Dilution" ** testing if installed package keeps a record of temporary installation path * DONE (affydata) * installing *source* package ‘hgu95av2cdf’ ... ** this is package ‘hgu95av2cdf’ version ‘2.18.0’ ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu95av2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu95av2cdf’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu95av2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu95av2cdf’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu95av2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu95av2cdf’ ** testing if installed package keeps a record of temporary installation path * DONE (hgu95av2cdf) * installing *source* package ‘RandVar’ ... ** this is package ‘RandVar’ version ‘1.2.5’ ** package ‘RandVar’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 * DONE (RandVar) begin installing package ‘distrMod’ * installing *source* package ‘illuminaHumanv3.db’ ... ** this is package ‘illuminaHumanv3.db’ version ‘1.26.0’ ** using staged installation ** 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 * DONE (illuminaHumanv3.db) * installing *source* package ‘beadarray’ ... ** this is package ‘beadarray’ version ‘2.56.0’ ** package ‘beadarray’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpVHfXVs/R.INSTALL27fff12dec9c1b/beadarray/src' gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c BASH.c -o BASH.o gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c HULK.c -o HULK.o gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c determiningGridPositions.c -o determiningGridPositions.o gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c findAllOutliers.c -o findAllOutliers.o findAllOutliers.c: In function ‘findBeadStatus’: findAllOutliers.c:196:35: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized] 196 | if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){ | ~~~^~~~~~~~~~~~ findAllOutliers.c:155:16: note: ‘m’ was declared here 155 | double m, ma; | ^ findAllOutliers.c:189:15: warning: ‘ma’ may be used uninitialized [-Wmaybe-uninitialized] 189 | if(ma==0) { | ^ findAllOutliers.c:155:19: note: ‘ma’ was declared here 155 | double m, ma; | ^~ findAllOutliers.c: In function ‘findAllOutliers’: findAllOutliers.c:246:20: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized] 246 | free(status->validInds); | ~~~~~~^~~~~~~~~~~ findAllOutliers.c:226:27: note: ‘status’ was declared here 226 | beadStatusStruct *status; | ^~~~~~ gcc-14 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c imageProcessing.c -o imageProcessing.o imageProcessing.c: In function ‘illuminaBackground’: imageProcessing.c:88: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 88 | #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end) imageProcessing.c: In function ‘medianBackground’: imageProcessing.c:135: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 135 | #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end) imageProcessing.c: In function ‘illuminaSharpen’: imageProcessing.c:244: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 244 | #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2) imageProcessing.c:251: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 251 | #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2) gcc-14 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpVHfXVs/R.INSTALL27fff12dec9c1b/beadarray/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-beadarray/00new/beadarray/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (beadarray) begin installing package ‘beadarrayExampleData’ * installing *source* package ‘beadarrayExampleData’ ... ** this is package ‘beadarrayExampleData’ version ‘1.44.0’ ** using staged installation ** data ** inst ** help *** installing help indices ** building package indices ** installing vignettes ** 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 * DONE (beadarrayExampleData) * installing *source* package ‘distrMod’ ... ** this is package ‘distrMod’ version ‘2.9.7’ ** package ‘distrMod’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘norm’ in package ‘distrMod’ ** help *** installing help indices ** building package indices ** installing vignettes ** 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 * DONE (distrMod) begin installing package ‘RobAStBase’ * installing *source* package ‘RobAStBase’ ... ** this is package ‘RobAStBase’ version ‘1.2.7’ ** package ‘RobAStBase’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘clip’ in package ‘RobAStBase’ ** 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 * DONE (RobAStBase) begin installing package ‘RobLox’ * installing *source* package ‘RobLox’ ... ** this is package ‘RobLox’ version ‘1.2.3’ ** using staged installation ** 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 * DONE (RobLox) checking RobLox_1.2.3.tar.gz ... checking RobLoxBioC_1.2.2.tar.gz ... checking ROptEst_1.3.5.tar.gz ... Depends: Package: RobLox Depends: R(>= 3.4), stats, distrMod(>= 2.8.0), RobAStBase(>= 1.2.0) Imports: methods, lattice, RColorBrewer, Biobase, RandVar(>= 1.2.0), distr(>= 2.8.0) Timings: user system elapsed RobLox 93.601 6.664 102.527 Results: Check status summary: WARNING OK Source packages 0 1 Reverse depends 1 1 Check results summary: RobLox ... OK rdepends_RobLoxBioC ... WARNING * checking R code for possible problems ... [25s/25s] WARNING rdepends_ROptEst ... OK