Wei Shi
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: devel |
| git_last_commit: 7de7817 |
| git_last_commit_date: 2025-07-30 02:02:59 -0400 (Wed, 30 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:13 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1819/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.23.3 (landing page) Wei Shi
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the Rsubread package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsubread.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Rsubread |
| Version: 2.23.3 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL Rsubread |
| StartedAt: 2025-07-31 20:20:16 -0000 (Thu, 31 Jul 2025) |
| EndedAt: 2025-07-31 20:21:19 -0000 (Thu, 31 Jul 2025) |
| EllapsedTime: 62.7 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.3’
** using staged installation
@@@@@ The operating system is Linux.
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c HelperFunctions.c -o HelperFunctions.o
In file included from HelperFunctions.c:56:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c LRMbase-index.c -o LRMbase-index.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c LRMchro-event.c -o LRMchro-event.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c LRMfile-io.c -o LRMfile-io.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c LRMhashtable.c -o LRMhashtable.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c LRMhelper.c -o LRMhelper.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c LRMseek-zlib.c -o LRMseek-zlib.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c R_wrapper.c -o R_wrapper.o
In file included from HelperFunctions.h:24,
from R_wrapper.c:35:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c RsimReads.c -o RsimReads.o
In file included from RsimReads.c:21:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c SNPCalling.c -o SNPCalling.o
In file included from SNPCalling.c:33:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c aligner.c -o aligner.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c atgcContent.c -o atgcContent.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c build-sam-index.c -o build-sam-index.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c cell-counts.c -o cell-counts.o
In file included from cell-counts.c:13:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
cell-counts.c: In function ‘cellCounts_args_context’:
cell-counts.c:721:2: warning: #warning "====== SHOULD REMOVE '* 4' BELOW =========" [-Wcpp]
721 | #warning "====== SHOULD REMOVE '* 4' BELOW ========="
| ^~~~~~~
cell-counts.c:724:2: warning: #warning "====== SHOULD REMOVE '+ 4' BELOW =========" [-Wcpp]
724 | #warning "====== SHOULD REMOVE '+ 4' BELOW ========="
| ^~~~~~~
cell-counts.c:816:26: warning: #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======" [-Wcpp]
816 | #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======"
| ^~~~~~~
cell-counts.c: In function ‘cellCounts_write_one_chroEvent’:
cell-counts.c:1134:47: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘int *’ [-Wformat=]
1134 | fprintf(wfp,"%s\t%d\t%d\t%s\t%d\n", chro, pos1, pos2, ce -> from_truth?"ANNOTATED":"NEW", ce -> step2_supported_reads);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int int *
| %ls
cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’:
cell-counts.c:1287:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
1287 | if(!ignore_GTF) cellCounts_add_or_update_chroEvent_in_table(cct_context, chroEvent_t_TYPE_EXON, chname_strand , start, end, 0, 1);
| ^~
cell-counts.c:1289:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
1289 | if(last_end>0){
| ^~
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_end_build_candidature_from_stacks’:
cell-counts.c:3227:29: warning: unused variable ‘x_candidate’ [-Wunused-variable]
3227 | int x_3end, x_5end, x_candidate;
| ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_build_junction_read_finalise_current_stack’:
cell-counts.c:3369:2: warning: #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn =============" [-Wcpp]
3369 | #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn ============="
| ^~~~~~~
cell-counts.c: In function ‘cellCounts_tree_iterative_search’:
cell-counts.c:3483:124: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=]
3483 | if(0)if(strstr(thread_context -> realignment_event_read_name ,"R00000895964"))fprintf(stderr,"REMOTE_TEST TYPE %d LEN %d (%d) REMOTE_loc_read = %d TO3=%d %s\n", envdtl -> event_type, inslen, (void*)envdtl -> length - NULL, remote_first_matching_base_read, to3end, thread_context -> realignment_event_read_name);
| ~^
| |
| int
| %ld
cell-counts.c:3438:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable]
3438 | 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:3788:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
3788 | for(x1=0; nch=result_cigar[x1] ; x1++){
| ^~~
cell-counts.c:3802:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
3802 | if(1) cellCounts_add_or_update_chroEvent_in_table(cct_context, chroEvent_t_TYPE_INDEL , chro_name, chro_pos -1, rposv, inslen_negative, 0); // thread safe
| ^~
cell-counts.c:3803:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
3803 | if(nch=='D') chro_cursor += tmpi;
| ^~
cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’:
cell-counts.c:3903:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable]
3903 | int rgap = -1;
| ^~~~
cell-counts.c:3933:26: warning: #warning "==== Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ====" [-Wcpp]
3933 | #warning "==== Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ===="
| ^~~~~~~
cell-counts.c:3943:37: warning: unused variable ‘manegative’ [-Wunused-variable]
3943 | int manegative = votetab -> masks[mai][maj];
| ^~~~~~~~~~
cell-counts.c:3855:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable]
3855 | int best_GTAG_negative = -1;
| ^~~~~~~~~~~~~~~~~~
cell-counts.c:3823:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable]
3823 | int i,j,reverse_text_offset, distinct_vote_number_i;
| ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:3823:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable]
3823 | 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:4034:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
4034 | while(nch = cigar[x1++]){
| ^~~
cell-counts.c:4096:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable]
4096 | int is_the_last, x2_not_matter;
| ^~~~~~~~~~~~~
cell-counts.c:4120:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
4120 | while(nch = cigar[x1++]){
| ^~~
cell-counts.c:4130:81: warning: array subscript has type ‘char’ [-Wchar-subscripts]
4130 | IVT_IntervalTreeNode * myroot = LR_roots[LRi];
| ^
cell-counts.c:4155:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
4155 | if(0)fprintf(stderr,"SUPP_NON query-cov %d ~ %d non-env-cov %d ~ %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , is_the_last?"SKIPPED":"ADDED");
| ~^ ~~~~~~~~~~~~
| | |
| int srInt_64 {aka long long int}
| %lld
cell-counts.c:4155:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=]
4155 | if(0)fprintf(stderr,"SUPP_NON query-cov %d ~ %d non-env-cov %d ~ %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , is_the_last?"SKIPPED":"ADDED");
| ~^
| |
| int
| %ld
cell-counts.c:4164:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
4164 | if(0)fprintf(stderr,"SUPP_X2TEST query-cov %d ~ %d non-env-cov %d ~ %d X2 %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , x2, (is_the_last && is_same_x2)?"SKIPPED":"ADDED");
| ~^ ~~~~~~~~~~~~
| | |
| int srInt_64 {aka long long int}
| %lld
cell-counts.c:4164:74: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=]
4164 | if(0)fprintf(stderr,"SUPP_X2TEST query-cov %d ~ %d non-env-cov %d ~ %d X2 %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , x2, (is_the_last && is_same_x2)?"SKIPPED":"ADDED");
| ~^
| |
| int
| %ld
cell-counts.c:4022:41: warning: unused variable ‘x3’ [-Wunused-variable]
4022 | int nch, tmpi=0, x1=0, b1off=0, x3;
| ^~
cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_cell’:
cell-counts.c:5140:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
5140 | fprintf( cct_context -> read_assignment_detail_fp, "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc), str1 -> umi, cct_context ->gene_name_array[gn]);\
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| void *
cell-counts.c:5158:41: note: in expansion of macro ‘ADD_count_hash’
5158 | ADD_count_hash(str1->cellbc, str1->gene_no,1);
| ^~~~~~~~~~~~~~
cell-counts.c:5140:95: note: format string is defined here
5140 | fprintf( cct_context -> read_assignment_detail_fp, "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc), str1 -> umi, cct_context ->gene_name_array[gn]);\
| ~^
| |
| char *
| %p
cell-counts.c:5205:148: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
5205 | fprintf( cct_context -> read_assignment_detail_fp, "FIX_UMI_SIMILAR\tSAMPLE%03d\t%s\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, acc_str -> cellbc), try_str -> umi, acc_str -> umi, cct_context ->gene_name_array[ acc_str -> gene_no ]);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| char * void *
| %p
cell-counts.c:5234:140: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
5234 | fprintf( cct_context -> read_assignment_detail_fp, "FIX_UMI_SIMILAR\tSAMPLE%03d\t%s\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, acc_str -> cellbc), try_str -> umi, acc_str -> umi, cct_context ->gene_name_array[ acc_str -> gene_no ]);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| char * void *
| %p
cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_step’:
cell-counts.c:5140:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
5140 | fprintf( cct_context -> read_assignment_detail_fp, "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc), str1 -> umi, cct_context ->gene_name_array[gn]);\
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| void *
cell-counts.c:5305:66: note: in expansion of macro ‘ADD_count_hash’
5305 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1);
| ^~~~~~~~~~~~~~
cell-counts.c:5140:95: note: format string is defined here
5140 | fprintf( cct_context -> read_assignment_detail_fp, "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc), str1 -> umi, cct_context ->gene_name_array[gn]);\
| ~^
| |
| char *
| %p
cell-counts.c: In function ‘cellCounts_find_nearest_gene_dist’:
cell-counts.c:6797:81: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
6797 | if(0)if( gene_name_list -> numOfElements )fprintf(stderr,"SUBADD_DIST of %lld, %s\n", gene_name_list -> numOfElements, gene_name_list -> elementList[0]);
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| char * void *
| %p
cell-counts.c: In function ‘cellCounts_write_final_junctions’:
cell-counts.c:6921:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable]
6921 | int unique_junctions = 0;
| ^~~~~~~~~~~~~~~~
cell-counts.c:6902:20: warning: unused variable ‘ky_i2’ [-Wunused-variable]
6902 | int ky_i1, ky_i2;
| ^~~~~
cell-counts.c:6902:13: warning: unused variable ‘ky_i1’ [-Wunused-variable]
6902 | int ky_i1, ky_i2;
| ^~~~~
cell-counts.c:6900:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable]
6900 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
| ^~~~~~~~~~~~~~
cell-counts.c:6869:13: warning: unused variable ‘infile_i’ [-Wunused-variable]
6869 | int infile_i, disk_is_full = 0;
| ^~~~~~~~
cell-counts.c: In function ‘cellCounts_release_context_from_align’:
cell-counts.c:2769:1: warning: control reaches end of non-void function [-Wreturn-type]
2769 | }
| ^
cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’:
cell-counts.c:3991:1: warning: control reaches end of non-void function [-Wreturn-type]
3991 | }
| ^
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:2231:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized]
2231 | if(search_start>0xffffff00) return;
| ^
cell-counts.c:2220:30: note: ‘search_start’ was declared here
2220 | unsigned int search_start, search_end, search_block_id;
| ^~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-bigtable.c -o core-bigtable.o
In file included from core.h:46,
from core-bigtable.c:12:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-indel.c -o core-indel.o
In file included from HelperFunctions.h:24,
from core-indel.c:28:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-interface-aligner.c -o core-interface-aligner.o
In file included from core-interface-aligner.c:7:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-interface-subjunc.c -o core-interface-subjunc.o
In file included from core-interface-subjunc.c:7:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-junction.c -o core-junction.o
In file included from core-junction.c:25:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
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 ){
| ^~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core.c -o core.o
In file included from core.c:45:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c detection-calls.c -o detection-calls.o
In file included from detection-calls.c:8:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
detection-calls.c: In function ‘DTCwrite_annotations’:
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};
| ^
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};
| ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c detectionCall.c -o detectionCall.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c detectionCallAnnotation.c -o detectionCallAnnotation.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c exon-algorithms.c -o exon-algorithms.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c exon-align-indel.c -o exon-align-indel.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c exon-align.c -o exon-align.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c flattenAnnotations.c -o flattenAnnotations.o
In file included from flattenAnnotations.c:41:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c fullscan.c -o fullscan.o
In file included from fullscan.c:26:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c fusion-align.c -o fusion-align.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c gen_rand_reads.c -o gen_rand_reads.o
In file included from gen_rand_reads.c:26:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c gene-algorithms.c -o gene-algorithms.o
In file included from gene-algorithms.c:36:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c gene-value-index.c -o gene-value-index.o
In file included from gene-value-index.h:24,
from gene-value-index.c:25:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
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 ))
| ^~
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);
| ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c hashtable.c -o hashtable.o
In file included from core.h:46,
from hashtable.c:18:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c index-builder.c -o index-builder.o
In file included from gene-value-index.h:24,
from index-builder.c:31:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c input-blc.c -o input-blc.o
In file included from input-blc.c:8:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
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);
| ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c input-files.c -o input-files.o
In file included from input-files.h:23,
from input-files.c:35:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
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];
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c interval_merge.c -o interval_merge.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c long-hashtable.c -o long-hashtable.o
In file included from core.h:46,
from long-hashtable.c:31:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c longread-mapping.c -o longread-mapping.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c mergeVCF.c -o mergeVCF.o
In file included from mergeVCF.c:7:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c processExons.c -o processExons.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c propmapped.c -o propmapped.o
In file included from propmapped.c:34:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c qualityScores.c -o qualityScores.o
In file included from qualityScores.c:27:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c read-repair.c -o read-repair.o
In file included from read-repair.c:6:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c readSummary.c -o readSummary.o
In file included from readSummary.c:41:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
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;
| ^~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c removeDupReads.c -o removeDupReads.o
In file included from removeDupReads.c:27:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c sam2bed.c -o sam2bed.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c sambam-file.c -o sambam-file.o
In file included from sambam-file.c:33:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c seek-zlib.c -o seek-zlib.o
In file included from core.h:46,
from seek-zlib.c:2:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c sorted-hashtable.c -o sorted-hashtable.o
In file included from sorted-hashtable.h:25,
from sorted-hashtable.c:20:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c sublog.c -o sublog.o
In file included from sublog.c:26:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c tx-unique.c -o tx-unique.o
In file included from tx-unique.h:4,
from tx-unique.c:6:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
| ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)