downloading reverse dependencies ... downloading distrDoc_2.8.2.tar.gz ... ok downloading RobAStBase_1.2.6.tar.gz ... ok downloading RobExtremes_1.3.0.tar.gz ... ok downloading RobLox_1.2.1.tar.gz ... ok downloading RobLoxBioC_1.2.2.tar.gz ... ok downloading ROptEst_1.3.4.tar.gz ... ok downloading distr_2.9.5.tar.gz ... ok downloading distrEllipse_2.8.3.tar.gz ... ok downloading distrRmetrics_2.8.2.tar.gz ... ok installing dependencies ‘affydata’, ‘beadarray’, ‘beadarrayExampleData’, ‘distrMod’, ‘distrSim’, ‘distrTeach’, ‘distrTEst’, ‘hgu95av2cdf’, ‘illuminaHumanv3.db’, ‘mvtnorm’, ‘RandVar’, ‘RobAStBase’, ‘RobAStRDA’, ‘RobLox’, ‘ROptEst’ also installing the dependencies ‘base64’, ‘BeadDataPackR’, ‘illuminaio’ begin installing package ‘base64’ begin installing package ‘BeadDataPackR’ begin installing package ‘RandVar’ begin installing package ‘distrSim’ begin installing package ‘distrTeach’ begin installing package ‘RobAStRDA’ begin installing package ‘affydata’ begin installing package ‘hgu95av2cdf’ begin installing package ‘illuminaHumanv3.db’ begin installing package ‘mvtnorm’ * installing *source* package ‘base64’ ... ** 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’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLMLgpg/R.INSTALL1777f953069ac0/BeadDataPackR/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/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-d-gcc-14/lib -Wl,-O1 -o BeadDataPackR.so BeadDataPackR.o R_init_BeadDataPackR.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLMLgpg/R.INSTALL1777f953069ac0/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’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpE4h03s/R.INSTALL1778a6516220c4/illuminaio/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/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-d-gcc-14/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-d-gcc-14/lib -Wl,-O1 -o illuminaio.so 000.init.o des.o local_des.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpE4h03s/R.INSTALL1778a6516220c4/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’ ... ** 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 ‘distrTeach’ ... ** package ‘distrTeach’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (distrTeach) * installing *source* package ‘mvtnorm’ ... ** package ‘mvtnorm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpiyXD6F/R.INSTALL17780574b42e11/mvtnorm/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lpmvnorm.c -o lpmvnorm.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ltMatrices.c -o ltMatrices.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c miwa.c -o miwa.o gfortran-14 -fpic -g -O2 -Wall -mtune=native -c mvt.f -o mvt.o mvt.f:868:11: 868 | hs = sign( one, dh - r*dk ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] mvt.f:869:11: 869 | ks = sign( one, dk - r*dh ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] mvt.f:1164:16: 1164 | K = MOD( C(NP, MIN(NDIM-1,KLIM-1))*DBLE(K), DBLE(P(NP)) ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] mvt.f:1224:17: 1224 | JP = 1 + J*R(J) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mvtnorm-init.c -o mvtnorm-init.o gfortran-14 -fpic -g -O2 -Wall -mtune=native -c tvpack.f -o tvpack.o tvpack.f:395:14: 395 | HS = SIGN( ONE, DH - R*DK ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] tvpack.f:396:14: 396 | KS = SIGN( ONE, DK - R*DH ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] tvpack.f:220:72: 220 | END | ^ Warning: ‘fin’ may be used uninitialized [-Wmaybe-uninitialized] tvpack.f:196:58: 196 | DOUBLE PRECISION EI(NL), AI(NL), BI(NL), FI(NL), FIN, ERR, KRNRDT | ^ note: ‘fin’ was declared here gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o mvtnorm.so C_FORTRAN_interface.o lpmvnorm.o ltMatrices.o miwa.o mvt.o mvtnorm-init.o tvpack.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpiyXD6F/R.INSTALL17780574b42e11/mvtnorm/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mvtnorm/00new/mvtnorm/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 (mvtnorm) * installing *source* package ‘RobAStRDA’ ... ** package ‘RobAStRDA’ 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 ** 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 (RobAStRDA) * installing *source* package ‘hgu95av2cdf’ ... ** 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 ‘distrSim’ ... ** package ‘distrSim’ 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 ‘simulate’ in package ‘distrSim’ ** 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 (distrSim) begin installing package ‘distrTEst’ * installing *source* package ‘RandVar’ ... ** 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’ ... ** 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 ‘distrTEst’ ... ** package ‘distrTEst’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (distrTEst) * installing *source* package ‘beadarray’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpo3gjF9/R.INSTALL177976176a58ed/beadarray/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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-d-gcc-14/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-d-gcc-14/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-d-gcc-14/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-d-gcc-14/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-d-gcc-14/lib -Wl,-O1 -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpo3gjF9/R.INSTALL177976176a58ed/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’ ... ** 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’ ... ** 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’ ... ** 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 ‘ROptEst’ begin installing package ‘RobLox’ * installing *source* package ‘RobLox’ ... ** package ‘RobLox’ 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 ** 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) * installing *source* package ‘ROptEst’ ... ** package ‘ROptEst’ 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 ** 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 (ROptEst) checking distrMod_2.9.4.tar.gz ... checking distrDoc_2.8.2.tar.gz ... checking RobAStBase_1.2.6.tar.gz ... checking RobExtremes_1.3.0.tar.gz ... checking RobLox_1.2.1.tar.gz ... checking RobLoxBioC_1.2.2.tar.gz ... checking ROptEst_1.3.4.tar.gz ... checking distr_2.9.5.tar.gz ... checking distrEllipse_2.8.3.tar.gz ... checking distrRmetrics_2.8.2.tar.gz ... Depends: Package: distrMod Depends: R(>= 3.4), distr(>= 2.8.0), distrEx(>= 2.8.0), RandVar(>= 1.2.0), MASS, stats4, methods Imports: startupmsg, sfsmisc, graphics, stats, grDevices Timings: user system elapsed distrMod 128.577 6.864 136.365 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 1 8 Check results summary: distrMod ... NOTE * checking CRAN incoming feasibility ... [5s/6s] NOTE rdepends_distr ... OK rdepends_distrDoc ... OK rdepends_distrEllipse ... OK rdepends_distrRmetrics ... OK rdepends_RobAStBase ... OK rdepends_RobExtremes ... NOTE * checking Rd cross-references ... NOTE rdepends_RobLox ... OK rdepends_RobLoxBioC ... OK rdepends_ROptEst ... OK Warning in normalizePath(dir) : path[1]="/home/hornik/tmp/CRAN": No such file or directory Calls: -> normalizePath Warning in normalizePath(dir) : path[1]="/home/hornik/tmp/CRAN": No such file or directory Calls: -> R_check_outdirs -> normalizePath