############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rsubread ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'Rsubread' ... ** using staged installation @@@@@ The operating system is Windows. ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c HelperFunctions.c -o HelperFunctions.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c LRMbase-index.c -o LRMbase-index.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c LRMchro-event.c -o LRMchro-event.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c LRMfile-io.c -o LRMfile-io.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c LRMhashtable.c -o LRMhashtable.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c LRMhelper.c -o LRMhelper.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c LRMseek-zlib.c -o LRMseek-zlib.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_wrapper.c -o R_wrapper.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RsimReads.c -o RsimReads.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c SNPCalling.c -o SNPCalling.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c aligner.c -o aligner.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c atgcContent.c -o atgcContent.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c build-sam-index.c -o build-sam-index.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c cell-counts.c -o cell-counts.o cell-counts.c: In function 'cellCounts_sort_feature_info': cell-counts.c:1042:6: warning: unused variable 'curr_chro_number' [-Wunused-variable] int curr_chro_number = 0; ^~~~~~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_parallel_gzip_writer_add_read_fqs_scRNA': cell-counts.c:1752:6: warning: unused variable 'x1' [-Wunused-variable] int x1=0; ^~ cell-counts.c: In function 'cellCounts_vote_and_add_count': cell-counts.c:1818:6: warning: unused variable 'fields' [-Wunused-variable] int fields = cellCounts_scan_read_name_str(cct_context, NULL, read_name, &sample_seq, &sample_qual, &BC_seq, &BC_qual, &UMI_seq, &UMI_qual, &lane_str, &RG, &rname_trimmed_len); ^~~~~~ cell-counts.c: In function 'cellCounts_prepare_context_for_align': cell-counts.c:1970:30: warning: unused variable 'thread_context' [-Wunused-variable] cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no; ^~~~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_fetch_next_read_pair': cell-counts.c:2067:6: warning: unused variable 'lockret2' [-Wunused-variable] int lockret2=cellCounts_lock_release(&cct_context -> input_dataset_lock); ^~~~~~~~ cell-counts.c:2053:6: warning: unused variable 'lockret1' [-Wunused-variable] int lockret1=cellCounts_lock_occupy(&cct_context -> input_dataset_lock); ^~~~~~~~ cell-counts.c: In function 'cellCounts_indel_recorder_copy': cell-counts.c:2156:17: warning: array subscript has type 'char' [-Wchar-subscripts] for(sri=votrec[toli]; sri<=votrec[toli+1]; sri++) offsets[sri -1] = votrec[toli+2]; ^ cell-counts.c:2159:13: warning: array subscript has type 'char' [-Wchar-subscripts] if(offsets[sri]!=0x77){ ^ cell-counts.c:2160:26: warning: array subscript has type 'char' [-Wchar-subscripts] *read_pos_move=offsets[sri]; ^ cell-counts.c:2168:13: warning: array subscript has type 'char' [-Wchar-subscripts] if(offsets[sri]!=0x77){ ^ cell-counts.c:2169:11: warning: array subscript has type 'char' [-Wchar-subscripts] offsets[sri] -= (*read_pos_move); ^ cell-counts.c:2172:25: warning: array subscript has type 'char' [-Wchar-subscripts] offset_cur = offsets[sri]; ^ cell-counts.c:2174:29: warning: array subscript has type 'char' [-Wchar-subscripts] high_conf_index = offsets[sri]; ^ cell-counts.c:2176:27: warning: array subscript has type 'char' [-Wchar-subscripts] if(offset_cur != offsets[sri] && subread0>0){ ^ cell-counts.c:2177:10: warning: array subscript has type 'char' [-Wchar-subscripts] alnrec[toli]= subread0; ^ cell-counts.c:2181:24: warning: array subscript has type 'char' [-Wchar-subscripts] offset_cur = offsets[sri]; ^ cell-counts.c:2189:13: warning: array subscript has type 'char' [-Wchar-subscripts] if(offsets[sri]==0x77) subread0 =-1; ^ cell-counts.c:2192:11: warning: array subscript has type 'char' [-Wchar-subscripts] alnrec[toli]= subread0; ^ cell-counts.c:2203:21: warning: array subscript has type 'char' [-Wchar-subscripts] for(toli=0; alnrec[toli]; toli+=3){ ^ cell-counts.c:2204:51: warning: array subscript has type 'char' [-Wchar-subscripts] SUBREADprintf(" %d ~ %d : indels=%d\n", alnrec[toli], alnrec[toli+1], alnrec[toli+2]); ^ cell-counts.c: In function 'cellCounts_explain_one_read': cell-counts.c:2345:16: warning: unused variable 'meet_end' [-Wunused-variable] unsigned int meet_end = abs_pos + first_correct_base + indel_offset; ^~~~~~~~ cell-counts.c:2315:6: warning: unused variable 'indels_in_highconf' [-Wunused-variable] int indels_in_highconf = cellCounts_indel_recorder_copy(indel_offsets, votetab -> indel_recorder[vote_i][vote_j], tolimax, all_subreads, &read_pos_move, read_name, abs_pos); ^~~~~~~~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_select_and_write_alignments': cell-counts.c:2437:18: warning: unused variable 'topbuf' [-Wunused-variable] topK_buffer_t * topbuf = &thread_context->topKbuff; ^~~~~~ cell-counts.c: In function 'cellCounts_process_copy_ptrs_to_votes': cell-counts.c:2600:7: warning: unused variable 'subread_number_P1' [-Wunused-variable] int subread_number_P1 = 1+((myno >= applied_subreads_per_strand)?myno - applied_subreads_per_strand:myno); ^~~~~~~~~~~~~~~~~ cell-counts.c: In function 'simpleMode_cellCounts_process_copy_ptrs_to_votes': cell-counts.c:2722:7: warning: unused variable 'subread_number_P1' [-Wunused-variable] int subread_number_P1 = 1+((myno >= applied_subreads_per_strand)?myno - applied_subreads_per_strand:myno); ^~~~~~~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_do_voting': cell-counts.c:2881:15: warning: unused variable 'high_index_border' [-Wunused-variable] unsigned int high_index_border = cct_context -> value_index -> start_base_offset + cct_context -> value_index -> length; ^~~~~~~~~~~~~~~~~ cell-counts.c:2880:15: warning: unused variable 'low_index_border' [-Wunused-variable] unsigned int low_index_border = cct_context -> value_index -> start_base_offset; ^~~~~~~~~~~~~~~~ cell-counts.c:2868:30: warning: unused variable 'thread_context' [-Wunused-variable] cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no; ^~~~~~~~~~~~~~ cell-counts.c:2866:6: warning: unused variable 'sqr_interval' [-Wunused-variable] int sqr_interval=10000; ^~~~~~~~~~~~ cell-counts.c:2860:6: warning: unused variable 'xk1' [-Wunused-variable] int xk1; ^~~ cell-counts.c: In function 'simpleMode_cellCounts_do_voting': cell-counts.c:3028:9: warning: variable 'building_rbin_offset' set but not used [-Wunused-but-set-variable] int building_rbin_offset = 0, read_text_rev_offset =0; ^~~~~~~~~~~~~~~~~~~~ cell-counts.c:2988:15: warning: unused variable 'high_index_border' [-Wunused-variable] unsigned int high_index_border = cct_context -> value_index -> start_base_offset + cct_context -> value_index -> length; ^~~~~~~~~~~~~~~~~ cell-counts.c:2987:15: warning: unused variable 'low_index_border' [-Wunused-variable] unsigned int low_index_border = cct_context -> value_index -> start_base_offset; ^~~~~~~~~~~~~~~~ cell-counts.c:2971:6: warning: unused variable 'sqr_interval' [-Wunused-variable] int sqr_interval=10000; ^~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_merge_batches_worker': cell-counts.c:3651:35: warning: pointer targets in assignment from 'char *' to 'Bytef *' {aka 'unsigned char *'} differ in signedness [-Wpointer-sign] my_current_job -> strm.next_in = inbin_blk ; ^ cell-counts.c: In function 'cellCounts_save_BAM_result': cell-counts.c:3989:89: warning: statement with no effect [-Wunused-value] if(CELLCOUNTS_BAMBLOCK_COMP_NUMBER>1)finished_job -> task -> inbin_batch_start_offsets[1]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ cell-counts.c: In function 'cellCounts_merged_45K_to_90K_sum_WRT': cell-counts.c:4114:14: warning: unused variable 'sorted_order_p1_to_i_p1_tab' [-Wunused-variable] HashTable * sorted_order_p1_to_i_p1_tab = vp2[1]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:4113:14: warning: unused variable 'loaded_features' [-Wunused-variable] ArrayList * loaded_features = vp2[0]; ^~~~~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_merged_write_nozero_geneids_WRT': cell-counts.c:4149:14: warning: unused variable 'sorted_order_p1_to_i_p1_tab' [-Wunused-variable] HashTable * sorted_order_p1_to_i_p1_tab = tv2[1]; ^~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c: In function 'delete_file_thread': cell-counts.c:4351:3: warning: implicit declaration of function 'sleep'; did you mean '_sleep'? [-Wimplicit-function-declaration] sleep(2); ^~~~~ _sleep cell-counts.c:4346:44: warning: '%06d' directive writing between 6 and 11 bytes into a region of size between 4 and 1003 [-Wformat-overflow=] sprintf(tmp_fname, "%s/temp-cellcounts-%06d-%03d.tmpbin", cct_context -> temp_file_dir, getpid(), x1); ^~~~ cell-counts.c:4346:24: note: directive argument in the range [0, 151] sprintf(tmp_fname, "%s/temp-cellcounts-%06d-%03d.tmpbin", cct_context -> temp_file_dir, getpid(), x1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:4346:5: note: 'sprintf' output between 35 and 1039 bytes into a destination of size 1020 sprintf(tmp_fname, "%s/temp-cellcounts-%06d-%03d.tmpbin", cct_context -> temp_file_dir, getpid(), x1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_open_cellbc_batches': cell-counts.c:1185:20: warning: '/temp-cellcounts-' directive writing 17 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] sprintf(fname,"%s/temp-cellcounts-%06d-%03d.tmpbin",cct_context->temp_file_dir,getpid(), x1); ^~~~~~~~~~~~~~~~~ cell-counts.c:1185:17: note: directive argument in the range [0, 151] sprintf(fname,"%s/temp-cellcounts-%06d-%03d.tmpbin",cct_context->temp_file_dir,getpid(), x1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:1185:3: note: 'sprintf' output between 35 and 1039 bytes into a destination of size 1000 sprintf(fname,"%s/temp-cellcounts-%06d-%03d.tmpbin",cct_context->temp_file_dir,getpid(), x1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_find_hits_for_mapped_section': cell-counts.c:1456:7: warning: 'search_start' may be used uninitialized in this function [-Wmaybe-uninitialized] int search_start, search_end, search_block_id; ^~~~~~~~~~~~ cell-counts.c: In function 'cellCounts_save_BAM_result': cell-counts.c:3995:122: warning: array subscript 2 is above array bounds of 'int[1]' [-Warray-bounds] if(outblocki < finished_job -> task -> inbin_number -1)nextoffset = finished_job -> task -> inbin_batch_start_offsets[outblocki +1]; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c core-bigtable.c -o core-bigtable.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c core-indel.c -o core-indel.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c core-interface-aligner.c -o core-interface-aligner.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c core-interface-subjunc.c -o core-interface-subjunc.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c core-junction.c -o core-junction.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c core.c -o core.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c detection-calls.c -o detection-calls.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c detectionCall.c -o detectionCall.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c detectionCallAnnotation.c -o detectionCallAnnotation.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c exon-algorithms.c -o exon-algorithms.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c exon-align-indel.c -o exon-align-indel.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c exon-align.c -o exon-align.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c flattenAnnotations.c -o flattenAnnotations.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fullscan.c -o fullscan.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c fusion-align.c -o fusion-align.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c gen_rand_reads.c -o gen_rand_reads.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c gene-algorithms.c -o gene-algorithms.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c gene-value-index.c -o gene-value-index.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c hashtable.c -o hashtable.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c index-builder.c -o index-builder.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c input-blc.c -o input-blc.o input-blc.c: In function 'cacheBCL_qualTest_BAMmode': input-blc.c:1006:53: warning: variable 'lane_str' set but not used [-Wunused-but-set-variable] char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL; ^~~~~~~~ input-blc.c:1006:31: warning: variable 'sample_barcode' set but not used [-Wunused-but-set-variable] char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL; ^~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c input-files.c -o input-files.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c interval_merge.c -o interval_merge.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c long-hashtable.c -o long-hashtable.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c longread-mapping.c -o longread-mapping.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c mergeVCF.c -o mergeVCF.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c processExons.c -o processExons.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c propmapped.c -o propmapped.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c qualityScores.c -o qualityScores.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c read-repair.c -o read-repair.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c readSummary.c -o readSummary.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c removeDupReads.c -o removeDupReads.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c sam2bed.c -o sam2bed.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c sambam-file.c -o sambam-file.o sambam-file.c: In function 'SamBam_writer_sort_bins_to_BAM': sambam-file.c:2379:24: warning: variable 'last_written_BAI_chro' set but not used [-Wunused-but-set-variable] int old_chro_no = -1, last_written_BAI_chro = -1; ^~~~~~~~~~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c seek-zlib.c -o seek-zlib.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c sorted-hashtable.c -o sorted-hashtable.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c sublog.c -o sublog.o "C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c tx-unique.c -o tx-unique.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rsubread/00new/Rsubread/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Rsubread' finding HTML links ... done RsubreadUsersGuide html align html atgcContent html buildindex html cellCounts html detectionCall html detectionCallAnnotation html exactSNP html featureCounts html findCommonVariants html flattenGTF html getInBuiltAnnotation html processExons html promoterRegions html propmapped html qualityScores html removeDupReads html repair html sam2bed html simReads html sublong html txUnique html ** 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 (Rsubread) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'HDTD' is missing or broken done