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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Rsubread_2.25.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.25.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsubread’ can be installed ... WARNING
Found the following significant warnings:
  cell-counts.c:5665:78: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
  cell-counts.c:5665:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 8 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
  cell-counts.c:6501:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.23-bioc/meat/Rsubread.Rcheck/00install.out’ for details.
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is 39.6Mb
  sub-directories of 1Mb or more:
    annot  30.9Mb
    libs    3.8Mb
    qualf   3.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'cellCounts.Rd':
cellCounts
  Code: function(index, sample, input.mode = "BCL", cell.barcode =
                 NULL, nsubreads = 15, minVotes = 1, maxMismatches =
                 10, minMappedLength = 1, annot.inbuilt = "mm39",
                 annot.ext = NULL, isGTFAnnotationFile = FALSE,
                 GTF.featureType = "exon", GTF.attrType = "gene_id",
                 useMetaFeatures = TRUE, detectJunctions = FALSE,
                 umi.cutoff = NULL, nthreads = 10, nBestLocations = 1,
                 uniqueMapping = FALSE, reportExcludedBarcodes = FALSE,
                 barcoding.mode = "Chromium", cell.level.junctions =
                 NULL, cell.cluster.map = NULL, enableSoftClipping =
                 TRUE)
  Docs: function(index, sample, input.mode = "BCL", cell.barcode =
                 NULL, nsubreads = 15, minVotes = 1, maxMismatches =
                 10, minMappedLength = 1, annot.inbuilt = "mm39",
                 annot.ext = NULL, isGTFAnnotationFile = FALSE,
                 GTF.featureType = "exon", GTF.attrType = "gene_id",
                 useMetaFeatures = TRUE, detectJunctions = FALSE,
                 umi.cutoff = NULL, nthreads = 10, nBestLocations = 1,
                 uniqueMapping = FALSE, reportExcludedBarcodes = FALSE)
  Argument names in code not in docs:
    barcoding.mode cell.level.junctions cell.cluster.map
    enableSoftClipping

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/Rsubread/libs/Rsubread.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
propmapped 29.269 16.024  47.148
align      28.330 16.450  44.907
sublong    24.373  4.096  28.396
buildindex  9.385  1.413  13.158
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/Rsubread.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Rsubread
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.25.2’
** 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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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:1185:16: warning: unused variable ‘params’ [-Wunused-variable]
 1185 |         void * params [5];
      |                ^~~~~~
cell-counts.c: In function ‘cellCounts_add_or_update_chroEvent_in_table’:
cell-counts.c:1268:23: warning: variable ‘new_details’ set but not used [-Wunused-but-set-variable]
 1268 |         chroEvent_t * new_details = NULL;
      |                       ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’:
cell-counts.c:1322:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable]
 1322 |         int last_end = -1, last_start = -1;
      |                            ^~~~~~~~~~
cell-counts.c: In function ‘cellCounts_register_junc_feature’:
cell-counts.c:1528:30: warning: unused variable ‘sample_i’ [-Wunused-variable]
 1528 |         int xk1, edge_tab_i, sample_i;
      |                              ^~~~~~~~
cell-counts.c: In function ‘cellCounts_vote_and_add_count’:
cell-counts.c:2828:139: warning: unused variable ‘testi’ [-Wunused-variable]
 2828 |         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:3399:37: warning: unused variable ‘thread_context’ [-Wunused-variable]
 3399 |         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:3521:29: warning: unused variable ‘cigar_rlen’ [-Wunused-variable]
 3521 |                         int cigar_rlen = cellCounts_reduce_Cigar(cigar_being_built,final_cigar,&sum_ins);
      |                             ^~~~~~~~~~
cell-counts.c:3475:29: warning: unused variable ‘x_candidate’ [-Wunused-variable]
 3475 |         int x_3end, x_5end, x_candidate;
      |                             ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_tree_iterative_search’:
cell-counts.c:3712:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable]
 3712 |                 int read_for_testing_len = edge_region_end - edge_region_start +1;
      |                     ^~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_explain_one_alignment’:
cell-counts.c:3817:139: warning: unused variable ‘testi’ [-Wunused-variable]
 3817 |         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_add_covered_indels_in_table’:
cell-counts.c:4098:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 4098 | 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:4099:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 4099 |                                 if(nch=='D') chro_cursor += tmpi;
      |                                 ^~
cell-counts.c:4080:13: warning: unused variable ‘retlen’ [-Wunused-variable]
 4080 |         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:4232:37: warning: unused variable ‘manegative’ [-Wunused-variable]
 4232 |                                 int manegative = votetab -> masks[mai][maj];
      |                                     ^~~~~~~~~~
cell-counts.c:4145:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable]
 4145 |                         int best_GTAG_negative = -1;
      |                             ^~~~~~~~~~~~~~~~~~
cell-counts.c:4115:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable]
 4115 |         int i,j,reverse_text_offset, distinct_vote_number_i;
      |                                      ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4115:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable]
 4115 |         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:4360:37: warning: variable ‘on_chro_len’ set but not used [-Wunused-but-set-variable]
 4360 |                                 int on_chro_len = tmpi +1;
      |                                     ^~~~~~~~~~~
cell-counts.c:4391:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable]
 4391 |                                                 int is_the_last, x2_not_matter;
      |                                                                  ^~~~~~~~~~~~~
cell-counts.c:4425:81: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 4425 |                                         IVT_IntervalTreeNode * myroot = LR_roots[LRi];
      |                                                                                 ^
cell-counts.c:4315:41: warning: unused variable ‘x3’ [-Wunused-variable]
 4315 |         int nch, tmpi=0, x1=0, b1off=0, x3;
      |                                         ^~
cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_step’:
cell-counts.c:5665:78: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
 5665 | fprintf(stderr,"STEP_%d_FINN_X1: %.10s  gene_no=%016lld  supReads=%d  start=%d,%d  CELL_BC=%d CHANGED=%d\n", is_UMI_step2+1, str1->umi, str1 -> gene_no, str1->supp_reads,x1, sec_start, str1->cellbc, is_umi_changed);
      |                                                                             ~^                                                                                            ~~
      |                                                                              |                                                                                            |
      |                                                                              int                                                                                          srInt_64 {aka long long int}
      |                                                                             %lld
cell-counts.c:5665:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 8 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
 5665 | fprintf(stderr,"STEP_%d_FINN_X1: %.10s  gene_no=%016lld  supReads=%d  start=%d,%d  CELL_BC=%d CHANGED=%d\n", is_UMI_step2+1, str1->umi, str1 -> gene_no, str1->supp_reads,x1, sec_start, str1->cellbc, is_umi_changed);
      |                                                                                ~^                                                                                             ~~~~~~~~~
      |                                                                                 |                                                                                             |
      |                                                                                 int                                                                                           srInt_64 {aka long long int}
      |                                                                                %lld
cell-counts.c:5664:29: warning: unused variable ‘str2’ [-Wunused-variable]
 5664 | struct cell_gene_umi_supp * str2 = ArrayListGet(structs, sec_start +1);
      |                             ^~~~
cell-counts.c: In function ‘cellCounts_merged_bootstrap_a_sample’:
cell-counts.c:6501:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
 6501 | fprintf(stderr,"%dth resample: BOOT_30TH: %lld UMI / %lld cells. Top UMIs (original/resampled) %lld  %lld \n", x1, UMIs_30th_div10,  list_cellBCs_sorted_by_UMIs -> numOfElements, ori_umis , top_umis);
      |                 ~^                                                                                             ~~
      |                  |                                                                                             |
      |                  int                                                                                           srInt_64 {aka long long int}
      |                 %lld
cell-counts.c: In function ‘cellCounts_write_final_junctions’:
cell-counts.c:7399:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable]
 7399 |                 int unique_junctions = 0;
      |                     ^~~~~~~~~~~~~~~~
cell-counts.c:7378:20: warning: unused variable ‘ky_i2’ [-Wunused-variable]
 7378 |         int ky_i1, ky_i2;
      |                    ^~~~~
cell-counts.c:7378:13: warning: unused variable ‘ky_i1’ [-Wunused-variable]
 7378 |         int ky_i1, ky_i2;
      |             ^~~~~
cell-counts.c:7376:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable]
 7376 |         char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
      |                                                                                 ^~~~~~~~~~~~~~
cell-counts.c:7342:13: warning: unused variable ‘infile_i’ [-Wunused-variable]
 7342 |         int infile_i, disk_is_full = 0, sample_i;
      |             ^~~~~~~~
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:2386:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized]
 2386 |                 if(search_start>0xffffff00) return;
      |                   ^
cell-counts.c:2375:30: note: ‘search_start’ was declared here
 2375 |                 unsigned int search_start, search_end, search_block_id;
      |                              ^~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_write_final_other_events’:
cell-counts.c:7309:40: warning: array subscript -999 is below array bounds of ‘HashTable *[65]’ [-Warray-bounds=]
 7309 |         ArrayList * small_large_keys = HashTableKeys(cct_context -> chroEvent_detail_table[sample_i]);
      |                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:329:27: note: while referencing ‘chroEvent_detail_table’
  329 |         HashTable       * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1];
      |                           ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:7314:86: warning: array subscript -999 is below array bounds of ‘HashTable *[65]’ [-Warray-bounds=]
 7314 |                 chroEvent_t * ed = HashTableGet(cct_context -> chroEvent_detail_table[sample_i] , ArrayListGet(small_large_keys,x1));
      |                                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
cell-counts.c:329:27: note: while referencing ‘chroEvent_detail_table’
  329 |         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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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:585:59: warning: unused variable ‘npos’ [-Wunused-variable]
  585 |                                                 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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -g3  -fPIC  -g -O2  -Wall -Werror=format-security -c softclip-test.c -o softclip-test.o
softclip-test.c: In function ‘calculate_soft_clipping’:
softclip-test.c:42:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
   42 |         if(is_mismatch) free(is_mismatch); if(is_insertion) free(is_insertion);
      |         ^~
softclip-test.c:42:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
   42 |         if(is_mismatch) free(is_mismatch); if(is_insertion) free(is_insertion);
      |                                            ^~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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/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 softclip-test.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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)