Wei Shi
| Snapshot Date: 2025-10-09 13:45 -0400 (Thu, 09 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/Rsubread |
| git_branch: devel |
| git_last_commit: cadf5b3 |
| git_last_commit_date: 2025-10-08 00:10:13 -0400 (Wed, 08 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-10 12:07 -0400 (Fri, 10 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4854 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4642 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4587 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
| 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 1839/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rsubread 2.23.5 (landing page) Wei Shi
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 2.23.5 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL Rsubread |
| StartedAt: 2025-10-09 20:54:30 -0000 (Thu, 09 Oct 2025) |
| EndedAt: 2025-10-09 20:55:40 -0000 (Thu, 09 Oct 2025) |
| EllapsedTime: 70.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL Rsubread
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.5’
** 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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c HelperFunctions.c -o HelperFunctions.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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c R_wrapper.c -o R_wrapper.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c RsimReads.c -o RsimReads.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c SNPCalling.c -o SNPCalling.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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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:1141:16: warning: unused variable ‘params’ [-Wunused-variable]
1141 | void * params [5];
| ^~~~~~
cell-counts.c: In function ‘cellCounts_add_or_update_chroEvent_in_table’:
cell-counts.c:1222:23: warning: variable ‘new_details’ set but not used [-Wunused-but-set-variable]
1222 | chroEvent_t * new_details = NULL;
| ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’:
cell-counts.c:1261:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable]
1261 | int last_end = -1, last_start = -1;
| ^~~~~~~~~~
cell-counts.c: In function ‘cellCounts_register_junc_feature’:
cell-counts.c:1477:30: warning: unused variable ‘sample_i’ [-Wunused-variable]
1477 | int xk1, edge_tab_i, sample_i;
| ^~~~~~~~
cell-counts.c: In function ‘cellCounts_vote_and_add_count’:
cell-counts.c:2599:139: warning: unused variable ‘testi’ [-Wunused-variable]
2599 | 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:3161:37: warning: unused variable ‘thread_context’ [-Wunused-variable]
3161 | 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:3242:29: warning: unused variable ‘cigar_rlen’ [-Wunused-variable]
3242 | int cigar_rlen = cellCounts_reduce_Cigar(cigar_end5,final_cigar);
| ^~~~~~~~~~
cell-counts.c:3209:29: warning: unused variable ‘x_candidate’ [-Wunused-variable]
3209 | int x_3end, x_5end, x_candidate;
| ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_tree_iterative_search’:
cell-counts.c:3421:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable]
3421 | 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:3787:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
3787 | 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:3788:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
3788 | if(nch=='D') chro_cursor += tmpi;
| ^~
cell-counts.c:3769:13: warning: unused variable ‘retlen’ [-Wunused-variable]
3769 | 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:3884:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable]
3884 | int rgap = -1;
| ^~~~
cell-counts.c:3949:37: warning: unused variable ‘is_update’ [-Wunused-variable]
3949 | 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:3937:37: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable]
3937 | int rgap = -1;
| ^~~~
cell-counts.c:3924:37: warning: unused variable ‘manegative’ [-Wunused-variable]
3924 | int manegative = votetab -> masks[mai][maj];
| ^~~~~~~~~~
cell-counts.c:3836:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable]
3836 | int best_GTAG_negative = -1;
| ^~~~~~~~~~~~~~~~~~
cell-counts.c:3833:29: warning: variable ‘best_misma_no’ set but not used [-Wunused-but-set-variable]
3833 | int best_misma_no = -1;
| ^~~~~~~~~~~~~
cell-counts.c:3804:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable]
3804 | int i,j,reverse_text_offset, distinct_vote_number_i;
| ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:3804:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable]
3804 | 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:4047:37: warning: variable ‘on_chro_len’ set but not used [-Wunused-but-set-variable]
4047 | int on_chro_len = tmpi +1;
| ^~~~~~~~~~~
cell-counts.c:4078:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable]
4078 | int is_the_last, x2_not_matter;
| ^~~~~~~~~~~~~
cell-counts.c:4112:81: warning: array subscript has type ‘char’ [-Wchar-subscripts]
4112 | IVT_IntervalTreeNode * myroot = LR_roots[LRi];
| ^
cell-counts.c:4004:41: warning: unused variable ‘x3’ [-Wunused-variable]
4004 | 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:5162:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
5162 | 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:5180:41: note: in expansion of macro ‘ADD_count_hash’
5180 | ADD_count_hash(str1->cellbc, str1->gene_no,1);
| ^~~~~~~~~~~~~~
cell-counts.c:5162:95: note: format string is defined here
5162 | 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_do_one_batch_UMI_merge_one_step’:
cell-counts.c:5162:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
5162 | 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:5327:66: note: in expansion of macro ‘ADD_count_hash’
5327 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1);
| ^~~~~~~~~~~~~~
cell-counts.c:5162:95: note: format string is defined here
5162 | 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_write_final_junctions’:
cell-counts.c:6956:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable]
6956 | int unique_junctions = 0;
| ^~~~~~~~~~~~~~~~
cell-counts.c:6935:20: warning: unused variable ‘ky_i2’ [-Wunused-variable]
6935 | int ky_i1, ky_i2;
| ^~~~~
cell-counts.c:6935:13: warning: unused variable ‘ky_i1’ [-Wunused-variable]
6935 | int ky_i1, ky_i2;
| ^~~~~
cell-counts.c:6933:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable]
6933 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
| ^~~~~~~~~~~~~~
cell-counts.c:6899:13: warning: unused variable ‘infile_i’ [-Wunused-variable]
6899 | int infile_i, disk_is_full = 0, sample_i;
| ^~~~~~~~
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;
| ^~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_write_final_other_events’:
cell-counts.c:6866:40: warning: array subscript -999 is below array bounds of ‘HashTable *[41]’ [-Warray-bounds=]
6866 | ArrayList * small_large_keys = HashTableKeys(cct_context -> chroEvent_detail_table[sample_i]);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:316:27: note: while referencing ‘chroEvent_detail_table’
316 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1];
| ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:6871:86: warning: array subscript -999 is below array bounds of ‘HashTable *[41]’ [-Warray-bounds=]
6871 | chroEvent_t * ed = HashTableGet(cct_context -> chroEvent_detail_table[sample_i] , ArrayListGet(small_large_keys,x1));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
cell-counts.c:316:27: note: while referencing ‘chroEvent_detail_table’
316 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1];
| ^~~~~~~~~~~~~~~~~~~~~~
/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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-bigtable.c -o core-bigtable.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-indel.c -o core-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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-interface-aligner.c -o core-interface-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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core-interface-subjunc.c -o core-interface-subjunc.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 2.23.5\"" -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 ){
| ^~
/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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c core.c -o core.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 2.23.5\"" -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:155:109: 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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c flattenAnnotations.c -o flattenAnnotations.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c fullscan.c -o fullscan.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 2.23.5\"" -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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c gen_rand_reads.c -o gen_rand_reads.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c gene-algorithms.c -o gene-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 2.23.5\"" -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);
| ^~~~~~~~~~~~~
/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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c hashtable.c -o 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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c index-builder.c -o index-builder.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 2.23.5\"" -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);
| ^~~~
/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 2.23.5\"" -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];
| ^~~~~~~~
/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 2.23.5\"" -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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c long-hashtable.c -o long-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 2.23.5\"" -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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c mergeVCF.c -o mergeVCF.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 2.23.5\"" -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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c propmapped.c -o propmapped.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c qualityScores.c -o qualityScores.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c read-repair.c -o read-repair.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 2.23.5\"" -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;
| ^~~~~~~~~~~~~~~~~~~~~
/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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c removeDupReads.c -o removeDupReads.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 2.23.5\"" -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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c sambam-file.c -o sambam-file.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c seek-zlib.c -o seek-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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c sorted-hashtable.c -o sorted-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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c sublog.c -o sublog.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 2.23.5\"" -g3 -fPIC -g -O2 -Wall -Werror=format-security -c tx-unique.c -o tx-unique.o
/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)