Multiple platform build/check report for BioC 3.21 - INSTALL results for Rsubread on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
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*
INSTALL results for Rsubread on palomino7

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.
raw results
Summary

Package: Rsubread
Version: 2.21.1
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Rsubread
StartedAt: 2024-12-23 15:18:06 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 15:19:18 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 72.5 seconds
RetCode: 0
Status: OK
Command output

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###
### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Rsubread
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c HelperFunctions.c -o HelperFunctions.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LRMbase-index.c -o LRMbase-index.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LRMchro-event.c -o LRMchro-event.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LRMfile-io.c -o LRMfile-io.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LRMhashtable.c -o LRMhashtable.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LRMhelper.c -o LRMhelper.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_wrapper.c -o R_wrapper.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RsimReads.c -o RsimReads.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SNPCalling.c -o SNPCalling.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c aligner.c -o aligner.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c atgcContent.c -o atgcContent.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c build-sam-index.c -o build-sam-index.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cell-counts.c -o cell-counts.o
cell-counts.c: In function 'cellCounts_find_hits_for_mapped_section':
cell-counts.c:1622:19: warning: 'search_start' may be used uninitialized [-Wmaybe-uninitialized]
 1622 |                 if(search_start>0xffffff00) return;
      |                   ^
cell-counts.c:1611:30: note: 'search_start' was declared here
 1611 |                 unsigned int search_start, search_end, search_block_id;
      |                              ^~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c core-bigtable.c -o core-bigtable.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c core-indel.c -o core-indel.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c core-interface-aligner.c -o core-interface-aligner.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c core-junction.c -o core-junction.o
core-junction.c: In function 'find_donor_receptor':
core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2099 |                         if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0)
      |                         ^~
core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2103 |                                 if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){
      |                                 ^~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c core.c -o core.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c detection-calls.c -o detection-calls.o
detection-calls.c: In function 'DTCwrite_annotations':
detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=]
  155 |         DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:154:48: note: unnamed temporary defined here
  154 |         if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
      |                                                ^
detection-calls.c:155:109: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=]
  155 |         DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0);
      |                                                                                                             ^
detection-calls.c:154:48: note: unnamed temporary defined here
  154 |         if(!gc_2int) gc_2int = (unsigned int[]){0,0,0};
      |                                                ^
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c detectionCall.c -o detectionCall.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c exon-algorithms.c -o exon-algorithms.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c exon-align-indel.c -o exon-align-indel.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c exon-align.c -o exon-align.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c flattenAnnotations.c -o flattenAnnotations.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fullscan.c -o fullscan.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fusion-align.c -o fusion-align.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gen_rand_reads.c -o gen_rand_reads.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gene-algorithms.c -o gene-algorithms.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gene-value-index.c -o gene-value-index.o
gene-value-index.c: In function 'is_offset_in_chro':
gene-value-index.c:85:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   85 |                                 if( pos < chros -> padding  || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding ))
      |                                 ^~
In file included from gene-value-index.h:24,
                 from gene-value-index.c:25:
subread.h:153:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  153 | #define SUBREADprintf  msgqu_printf
      |                        ^~~~~~~~~~~~
gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf'
   87 |                                         SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos);
      |                                         ^~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hashtable.c -o hashtable.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c index-builder.c -o index-builder.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c input-blc.c -o input-blc.o
input-blc.c: In function 'iCache_continuous_read_lanes':
input-blc.c:580:59: warning: unused variable 'npos' [-Wunused-variable]
  580 |                                                 long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
      |                                                           ^~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:4834:50: warning: variable 'readname' set but not used [-Wunused-but-set-variable]
 4834 |         char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256];
      |                                                  ^~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c interval_merge.c -o interval_merge.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c long-hashtable.c -o long-hashtable.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c longread-mapping.c -o longread-mapping.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mergeVCF.c -o mergeVCF.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c processExons.c -o processExons.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c propmapped.c -o propmapped.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c qualityScores.c -o qualityScores.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read-repair.c -o read-repair.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readSummary.c -o readSummary.o
readSummary.c: In function 'vote_and_add_count':
readSummary.c:3777:58: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable]
 3777 |                                                 srInt_64 assignment_target_number = tmp_voter_id;
      |                                                          ^~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'fc_thread_merge_results':
readSummary.c:3847:32: warning: unused variable 'sample_i' [-Wunused-variable]
 3847 |         int xk1, xk2, ret = 0, sample_i;
      |                                ^~~~~~~~
readSummary.c: In function 'fc_write_final_junctions':
readSummary.c:5337:21: warning: unused variable 'unique_junctions' [-Wunused-variable]
 5337 |                 int unique_junctions = 0;
      |                     ^~~~~~~~~~~~~~~~
readSummary.c:5319:20: warning: unused variable 'ky_i2' [-Wunused-variable]
 5319 |         int ky_i1, ky_i2;
      |                    ^~~~~
readSummary.c:5319:13: warning: unused variable 'ky_i1' [-Wunused-variable]
 5319 |         int ky_i1, ky_i2;
      |             ^~~~~
readSummary.c:5317:81: warning: unused variable 'gene_name_tail' [-Wunused-variable]
 5317 |         char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
      |                                                                                 ^~~~~~~~~~~~~~
readSummary.c: In function 'readSummary':
readSummary.c:5516:52: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable]
 5516 |         int  isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
      |                                                    ^~~~~~~~~~~~~~~~~~
readSummary.c: In function 'register_junc_feature.part.0':
readSummary.c:839:35: warning: array subscript 'fc_junction_exon_in_transcript_t[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  839 |         new_item -> transcript_id = HashTableGetKey(global_context -> junction_transcript_table, transcript_id);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:838:55: note: object of size 8 allocated by 'calloc'
  838 |         fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1);
      |                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:841:43: warning: array subscript 'fc_junction_exon_in_transcript_t[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  841 |                 new_item -> transcript_id = strdup(transcript_id);
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:838:55: note: object of size 8 allocated by 'calloc'
  838 |         fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1);
      |                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:847:83: warning: array subscript 'fc_junction_exon_in_transcript_t[0]' is partly outside array bounds of 'unsigned char[8]' [-Warray-bounds=]
  847 |                 HashTablePut(global_context -> junction_transcript_table, new_item->transcript_id, new_txp);
      |                                                                           ~~~~~~~~^~~~~~~~~~~~~~~
readSummary.c:838:55: note: object of size 8 allocated by 'calloc'
  838 |         fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1);
      |                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'vote_and_add_count':
readSummary.c:3710:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized]
 3710 |                                         if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0;
      |                                            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c:3479:51: note: 'longest_overlap_score' was declared here
 3479 |                 int scoring_count = 0,  score_x1, longest_overlap_score;
      |                                                   ^~~~~~~~~~~~~~~~~~~~~
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c removeDupReads.c -o removeDupReads.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sam2bed.c -o sam2bed.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sambam-file.c -o sambam-file.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c seek-zlib.c -o seek-zlib.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sorted-hashtable.c -o sorted-hashtable.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sublog.c -o sublog.o
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tx-unique.c -o tx-unique.o
gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-Rsubread/00new/Rsubread/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsubread)