##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.8’
** using staged installation
@@@@@ The operating system is Linux.
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c HelperFunctions.c -o HelperFunctions.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMbase-index.c -o LRMbase-index.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMchro-event.c -o LRMchro-event.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMfile-io.c -o LRMfile-io.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMhashtable.c -o LRMhashtable.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMhelper.c -o LRMhelper.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c RsimReads.c -o RsimReads.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c SNPCalling.c -o SNPCalling.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c aligner.c -o aligner.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c atgcContent.c -o atgcContent.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c build-sam-index.c -o build-sam-index.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c cell-counts.c -o cell-counts.o
cell-counts.c: In function ‘cellCounts_write_junction_sumtable’:
cell-counts.c:1147:16: warning: unused variable ‘params’ [-Wunused-variable]
1147 | void * params [5];
| ^~~~~~
cell-counts.c: In function ‘cellCounts_add_or_update_chroEvent_in_table’:
cell-counts.c:1228:23: warning: variable ‘new_details’ set but not used [-Wunused-but-set-variable]
1228 | chroEvent_t * new_details = NULL;
| ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’:
cell-counts.c:1267:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable]
1267 | int last_end = -1, last_start = -1;
| ^~~~~~~~~~
cell-counts.c: In function ‘cellCounts_register_junc_feature’:
cell-counts.c:1483:30: warning: unused variable ‘sample_i’ [-Wunused-variable]
1483 | int xk1, edge_tab_i, sample_i;
| ^~~~~~~~
cell-counts.c: In function ‘cellCounts_vote_and_add_count’:
cell-counts.c:2605:139: warning: unused variable ‘testi’ [-Wunused-variable]
2605 | char * sample_seq=NULL, *sample_qual=NULL, *BC_qual=NULL, *BC_seq=NULL, *UMI_seq=NULL, *UMI_qual=NULL, *lane_str=NULL, *RG=NULL, *testi;
| ^~~~~
cell-counts.c: In function ‘cellCounts_convert_stack_to_cigar_str’:
cell-counts.c:3167:37: warning: unused variable ‘thread_context’ [-Wunused-variable]
3167 | cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
| ^~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_end_build_candidature_from_stacks’:
cell-counts.c:3248:29: warning: unused variable ‘cigar_rlen’ [-Wunused-variable]
3248 | int cigar_rlen = cellCounts_reduce_Cigar(cigar_end5,final_cigar);
| ^~~~~~~~~~
cell-counts.c:3215:29: warning: unused variable ‘x_candidate’ [-Wunused-variable]
3215 | int x_3end, x_5end, x_candidate;
| ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_tree_iterative_search’:
cell-counts.c:3427:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable]
3427 | int read_for_testing_len = edge_region_end - edge_region_start +1;
| ^~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_add_covered_indels_in_table’:
cell-counts.c:3793:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
3793 | if(1) cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_INDEL , chro_name, chro_pos -1, rposv, inslen_negative, 0); // thread safe
| ^~
cell-counts.c:3794:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
3794 | if(nch=='D') chro_cursor += tmpi;
| ^~
cell-counts.c:3775:13: warning: unused variable ‘retlen’ [-Wunused-variable]
3775 | int retlen = general_dynamic_align_moves_to_cigar(result_buffer, moved_len, result_cigar);
| ^~~~~~
cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’:
cell-counts.c:3890:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable]
3890 | int rgap = -1;
| ^~~~
cell-counts.c:3955:37: warning: unused variable ‘is_update’ [-Wunused-variable]
3955 | int is_update = cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_JUNCTION, machro, mapos, tstpos, 0, 0);//mapos and tstpos are just borrowed variables.
| ^~~~~~~~~
cell-counts.c:3943:37: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable]
3943 | int rgap = -1;
| ^~~~
cell-counts.c:3930:37: warning: unused variable ‘manegative’ [-Wunused-variable]
3930 | int manegative = votetab -> masks[mai][maj];
| ^~~~~~~~~~
cell-counts.c:3842:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable]
3842 | int best_GTAG_negative = -1;
| ^~~~~~~~~~~~~~~~~~
cell-counts.c:3839:29: warning: variable ‘best_misma_no’ set but not used [-Wunused-but-set-variable]
3839 | int best_misma_no = -1;
| ^~~~~~~~~~~~~
cell-counts.c:3810:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable]
3810 | int i,j,reverse_text_offset, distinct_vote_number_i;
| ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:3810:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable]
3810 | int i,j,reverse_text_offset, distinct_vote_number_i;
| ^~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_add_supported_unsupported_reads_from_cigar’:
cell-counts.c:4053:37: warning: variable ‘on_chro_len’ set but not used [-Wunused-but-set-variable]
4053 | int on_chro_len = tmpi +1;
| ^~~~~~~~~~~
cell-counts.c:4084:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable]
4084 | int is_the_last, x2_not_matter;
| ^~~~~~~~~~~~~
cell-counts.c:4118:81: warning: array subscript has type ‘char’ [-Wchar-subscripts]
4118 | IVT_IntervalTreeNode * myroot = LR_roots[LRi];
| ^
cell-counts.c:4010:41: warning: unused variable ‘x3’ [-Wunused-variable]
4010 | int nch, tmpi=0, x1=0, b1off=0, x3;
| ^~
cell-counts.c: In function ‘cellCounts_write_final_junctions’:
cell-counts.c:6961:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable]
6961 | int unique_junctions = 0;
| ^~~~~~~~~~~~~~~~
cell-counts.c:6940:20: warning: unused variable ‘ky_i2’ [-Wunused-variable]
6940 | int ky_i1, ky_i2;
| ^~~~~
cell-counts.c:6940:13: warning: unused variable ‘ky_i1’ [-Wunused-variable]
6940 | int ky_i1, ky_i2;
| ^~~~~
cell-counts.c:6938:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable]
6938 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
| ^~~~~~~~~~~~~~
cell-counts.c:6904:13: warning: unused variable ‘infile_i’ [-Wunused-variable]
6904 | int infile_i, disk_is_full = 0, sample_i;
| ^~~~~~~~
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:2237:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized]
2237 | if(search_start>0xffffff00) return;
| ^
cell-counts.c:2226:30: note: ‘search_start’ was declared here
2226 | unsigned int search_start, search_end, search_block_id;
| ^~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_write_final_other_events’:
cell-counts.c:6871:40: warning: array subscript -999 is below array bounds of ‘HashTable *[41]’ [-Warray-bounds=]
6871 | ArrayList * small_large_keys = HashTableKeys(cct_context -> chroEvent_detail_table[sample_i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:322:27: note: while referencing ‘chroEvent_detail_table’
322 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1];
| ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:6876:86: warning: array subscript -999 is below array bounds of ‘HashTable *[41]’ [-Warray-bounds=]
6876 | chroEvent_t * ed = HashTableGet(cct_context -> chroEvent_detail_table[sample_i] , ArrayListGet(small_large_keys,x1));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
cell-counts.c:322:27: note: while referencing ‘chroEvent_detail_table’
322 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1];
| ^~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-bigtable.c -o core-bigtable.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-indel.c -o core-indel.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-interface-aligner.c -o core-interface-aligner.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-junction.c -o core-junction.o
core-junction.c: In function ‘find_donor_receptor’:
core-junction.c:2099:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0)
| ^~
core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){
| ^~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core.c -o core.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c detection-calls.c -o detection-calls.o
detection-calls.c: In function ‘DTCwrite_annotations’:
detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
detection-calls.c:155:109: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
| ^
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=]
155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:154:48: note: unnamed temporary defined here
154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
| ^
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c detectionCall.c -o detectionCall.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-align-indel.c -o exon-align-indel.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-align.c -o exon-align.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c flattenAnnotations.c -o flattenAnnotations.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c fullscan.c -o fullscan.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c fusion-align.c -o fusion-align.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c gen_rand_reads.c -o gen_rand_reads.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c gene-algorithms.c -o gene-algorithms.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c gene-value-index.c -o gene-value-index.o
gene-value-index.c: In function ‘is_offset_in_chro’:
gene-value-index.c:85:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding ))
| ^~
In file included from gene-value-index.h:24,
from gene-value-index.c:25:
subread.h:153:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
153 | #define SUBREADprintf msgqu_printf
| ^~~~~~~~~~~~
gene-value-index.c:87:41: note: in expansion of macro ‘SUBREADprintf’
87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos);
| ^~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c hashtable.c -o hashtable.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c index-builder.c -o index-builder.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c input-blc.c -o input-blc.o
input-blc.c: In function ‘iCache_continuous_read_lanes’:
input-blc.c:580:59: warning: unused variable ‘npos’ [-Wunused-variable]
580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
| ^~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c input-files.c -o input-files.o
input-files.c: In function ‘reduce_SAM_to_BAM’:
input-files.c:3244:13: warning: unused variable ‘seq_len’ [-Wunused-variable]
3244 | int seq_len = qual - seq - 1;
| ^~~~~~~
input-files.c: In function ‘SAM_pairer_fix_format’:
input-files.c:4863:50: warning: variable ‘readname’ set but not used [-Wunused-but-set-variable]
4863 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256];
| ^~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c interval_merge.c -o interval_merge.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c long-hashtable.c -o long-hashtable.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c longread-mapping.c -o longread-mapping.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c mergeVCF.c -o mergeVCF.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c processExons.c -o processExons.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c propmapped.c -o propmapped.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c qualityScores.c -o qualityScores.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c read-repair.c -o read-repair.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c readSummary.c -o readSummary.o
readSummary.c: In function ‘vote_and_add_count’:
readSummary.c:3900:58: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable]
3900 | srInt_64 assignment_target_number = tmp_voter_id;
| ^~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function ‘fc_thread_merge_results’:
readSummary.c:3970:32: warning: unused variable ‘sample_i’ [-Wunused-variable]
3970 | int xk1, xk2, ret = 0, sample_i;
| ^~~~~~~~
readSummary.c: In function ‘fc_write_final_junctions’:
readSummary.c:5724:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable]
5724 | int unique_junctions = 0;
| ^~~~~~~~~~~~~~~~
readSummary.c:5700:20: warning: unused variable ‘ky_i2’ [-Wunused-variable]
5700 | int ky_i1, ky_i2;
| ^~~~~
readSummary.c:5700:13: warning: unused variable ‘ky_i1’ [-Wunused-variable]
5700 | int ky_i1, ky_i2;
| ^~~~~
readSummary.c:5698:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable]
5698 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
| ^~~~~~~~~~~~~~
readSummary.c: In function ‘readSummary’:
readSummary.c:5971:52: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable]
5971 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
| ^~~~~~~~~~~~~~~~~~
readSummary.c: In function ‘vote_and_add_count’:
readSummary.c:3833:66: warning: ‘longest_overlap_score’ may be used uninitialized [-Wmaybe-uninitialized]
3833 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:3602:51: note: ‘longest_overlap_score’ was declared here
3602 | int scoring_count = 0, score_x1, longest_overlap_score;
| ^~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c removeDupReads.c -o removeDupReads.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sam2bed.c -o sam2bed.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sambam-file.c -o sambam-file.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c seek-zlib.c -o seek-zlib.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sorted-hashtable.c -o sorted-hashtable.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sublog.c -o sublog.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.8\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c tx-unique.c -o tx-unique.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o Rsubread.so 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 -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rsubread/00new/Rsubread/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 (Rsubread)
