############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SparseArray ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘SparseArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o ExtendableJaggedArray.c: In function ‘_move_ExtendableJaggedArrays_to_SVT’: ExtendableJaggedArray.c:125:25: warning: ‘nzoffs_p’ may be used uninitialized in this function [-Wmaybe-uninitialized] 125 | free(nzoffs_p); | ^~~~~~~~~~~~~~ ExtendableJaggedArray.c:129:25: warning: ‘nzvals_p’ may be used uninitialized in this function [-Wmaybe-uninitialized] 129 | free(nzvals_p); | ^~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c OPBufTree.c -o OPBufTree.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Rvector_summarization.c -o Rvector_summarization.o Rvector_summarization.c:1309:12: warning: ‘count_NA_list_elts’ defined but not used [-Wunused-function] 1309 | static int count_NA_list_elts(SEXP x) | ^~~~~~~~~~~~~~~~~~ Rvector_summarization.c:1299:12: warning: ‘any_NA_list_elt’ defined but not used [-Wunused-function] 1299 | static int any_NA_list_elt(SEXP x) | ^~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Rvector_utils.c -o Rvector_utils.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SBT_utils.c -o SBT_utils.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_class.c -o SparseArray_class.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseMatrix_mult.c -o SparseMatrix_mult.o SparseMatrix_mult.c:372:13: warning: ‘crossprod2_doublemat_doubleSV’ defined but not used [-Wunused-function] 372 | static void crossprod2_doublemat_doubleSV( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SparseMatrix_mult.c:332:13: warning: ‘crossprod2_doubleSV_doublemat’ defined but not used [-Wunused-function] 332 | static void crossprod2_doubleSV_doublemat( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseVec_Math.c -o SparseVec_Math.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c coerceVector2.c -o coerceVector2.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c leaf_utils.c -o leaf_utils.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c matrixStats_methods.c -o matrixStats_methods.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c randomSparseArray.c -o randomSparseArray.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c readSparseCSV.c -o readSparseCSV.o readSparseCSV.c: In function ‘C_readSparseCSV_as_SVT_SparseMatrix’: readSparseCSV.c:248:25: warning: ‘nzoffs_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized] 248 | load_csv_data_to_AEbufs(data, data_len, col_idx - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 249 | nzvals_buf, nzoffs_buf); | ~~~~~~~~~~~~~~~~~~~~~~~ readSparseCSV.c:296:29: note: ‘nzoffs_buf’ was declared here 296 | IntAE *nzvals_buf, *nzoffs_buf; | ^~~~~~~~~~ readSparseCSV.c:248:25: warning: ‘nzvals_buf’ may be used uninitialized in this function [-Wmaybe-uninitialized] 248 | load_csv_data_to_AEbufs(data, data_len, col_idx - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 249 | nzvals_buf, nzoffs_buf); | ~~~~~~~~~~~~~~~~~~~~~~~ readSparseCSV.c:296:16: note: ‘nzvals_buf’ was declared here 296 | IntAE *nzvals_buf, *nzoffs_buf; | ^~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c rowsum_methods.c -o rowsum_methods.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c test.c -o test.o gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c thread_control.c -o thread_control.o gcc -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o OPBufTree.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Complex_methods.o SparseArray_Math_methods.o SparseArray_Ops_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_class.o SparseArray_dim_tuning.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o coerceVector2.o leaf_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray)