Rsubread 2.1.2
Wei Shi , Yang Liao and Gordon K Smyth
| Snapshot Date: 2020-04-13 17:00:10 -0400 (Mon, 13 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rsubread |
| Branch: master |
| Last Commit: aa7d0ba |
| Last Changed Date: 2020-02-17 22:35:15 -0400 (Mon, 17 Feb 2020) |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.1.2.tar.gz
###
##############################################################################
##############################################################################
install for i386
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o
detection-calls.c: In function 'DTCdo_add_feature':
detection-calls.c:52:2: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
strncpy(new_exon -> gene_name, gene_name, FEATURE_NAME_LENGTH);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:53:2: warning: 'strncpy' specified bound 200 equals destination size [-Wstringop-truncation]
strncpy(new_exon -> chro_name, chro_name, MAX_CHROMOSOME_NAME_LEN);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function 'bad_reverse_cigar':
gene-algorithms.c:2583:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
strncpy(ncg, ncg2, 99);
^~~~~~~~~~~~~~~~~~~~~~
gene-algorithms.c:2575:4: warning: 'strncat' output may be truncated copying 99 bytes from a string of length 99 [-Wstringop-truncation]
strncat(ncg2, ncg, 99);
^~~~~~~~~~~~~~~~~~~~~~
gene-algorithms.c:2576:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
strncpy(ncg, ncg2, 99);
^~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5267:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
C:/rtools40/mingw32/i686-w64-mingw32/include/stdlib.h:457:17: note: in a call to allocation function 'malloc' declared here
void *__cdecl malloc(size_t _Size);
^~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:46:46: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow]
the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o
readSummary.c: In function 'scRNA_merged_write_sparse_matrix':
readSummary.c:4412:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
fprintf(ofp_bcs,"%s\n", ArrayListGet(global_context -> scRNA_cell_barcodes_array, bc_no));
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%p
readSummary.c:4412:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
fprintf(ofp_bcs,"%s\n", ArrayListGet(global_context -> scRNA_cell_barcodes_array, bc_no));
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%p
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum_WRT':
readSummary.c:4493:21: warning: pointer targets in initialization of 'char *' from 'unsigned char *' differ in signedness [-Wpointer-sign]
char * gene_name = global_context -> gene_name_array[ kyGeneID - NULL-1 ];
^~~~~~~~~~~~~~
readSummary.c:4489:11: warning: unused variable 'sample_no' [-Wunused-variable]
srInt_64 sample_no = me -> counter1;
^~~~~~~~~
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum':
readSummary.c:4502:11: warning: unused variable 'x1' [-Wunused-variable]
srInt_64 x1;
^~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids_WRT':
readSummary.c:4521:22: warning: pointer targets in initialization of 'char *' from 'unsigned char *' differ in signedness [-Wpointer-sign]
char* gene_symbol = global_context -> gene_name_array [k-NULL-1];
^~~~~~~~~~~~~~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids':
readSummary.c:4529:11: warning: unused variable 'x1' [-Wunused-variable]
srInt_64 x1;
^~
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum':
readSummary.c:4506:31: warning: '.AmbSum' directive writing 7 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
sprintf(ofname,"%s.scRNA.%03d.AmbSum",global_context->input_file_name, sample_no+1);
^~~~~~~
readSummary.c:4506:2: note: 'sprintf' output between 18 and 1025 bytes into a destination of size 1020
sprintf(ofname,"%s.scRNA.%03d.AmbSum",global_context->input_file_name, sample_no+1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids':
readSummary.c:4527:31: warning: '.no0Genes' directive writing 9 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
sprintf(ofname,"%s.scRNA.%03d.no0Genes",global_context->input_file_name, samplenno+1);
^~~~~~~~~
readSummary.c:4527:2: note: 'sprintf' output between 20 and 1027 bytes into a destination of size 1020
sprintf(ofname,"%s.scRNA.%03d.no0Genes",global_context->input_file_name, samplenno+1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o
sambam-file.c: In function 'PBam_chunk_headers':
sambam-file.c:560:6: warning: 'strncpy' specified bound 100 equals destination size [-Wstringop-truncation]
strncpy(new_event->chro_name, chro_name, BAM_MAX_CHROMOSOME_NAME_LEN);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o
/mingw32/bin/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 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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/Rsubread.buildbin-libdir/00LOCK-Rsubread/00new/Rsubread/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rsubread'
finding HTML links ... done
RsubreadUsersGuide html
align html
atgcContent html
buildindex html
cellCounts html
detectionCall html
detectionCallAnnotation html
exactSNP html
featureCounts html
findCommonVariants html
flattenGTF html
getInBuiltAnnotation html
processExons html
promoterRegions html
propmapped html
qualityScores html
removeDupReads html
repair html
sam2bed html
simReads html
sublong html
txUnique html
** 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
install for x64
* installing *source* package 'Rsubread' ...
@@@@@ The operating system is Windows.
** libs
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c HelperFunctions.c -o HelperFunctions.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMbase-index.c -o LRMbase-index.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMchro-event.c -o LRMchro-event.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMfile-io.c -o LRMfile-io.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhashtable.c -o LRMhashtable.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMhelper.c -o LRMhelper.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMseek-zlib.c -o LRMseek-zlib.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_wrapper.c -o R_wrapper.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c RsimReads.c -o RsimReads.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c SNPCalling.c -o SNPCalling.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c aligner.c -o aligner.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c atgcContent.c -o atgcContent.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c build-sam-index.c -o build-sam-index.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-bigtable.c -o core-bigtable.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-indel.c -o core-indel.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-aligner.c -o core-interface-aligner.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-interface-subjunc.c -o core-interface-subjunc.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core-junction.c -o core-junction.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c core.c -o core.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detection-calls.c -o detection-calls.o
detection-calls.c: In function 'DTCdo_add_feature':
detection-calls.c:52:2: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
strncpy(new_exon -> gene_name, gene_name, FEATURE_NAME_LENGTH);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
detection-calls.c:53:2: warning: 'strncpy' specified bound 200 equals destination size [-Wstringop-truncation]
strncpy(new_exon -> chro_name, chro_name, MAX_CHROMOSOME_NAME_LEN);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCall.c -o detectionCall.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c detectionCallAnnotation.c -o detectionCallAnnotation.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-algorithms.c -o exon-algorithms.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align-indel.c -o exon-align-indel.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c exon-align.c -o exon-align.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flattenAnnotations.c -o flattenAnnotations.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fullscan.c -o fullscan.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fusion-align.c -o fusion-align.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gen_rand_reads.c -o gen_rand_reads.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function 'bad_reverse_cigar':
gene-algorithms.c:2583:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
strncpy(ncg, ncg2, 99);
^~~~~~~~~~~~~~~~~~~~~~
gene-algorithms.c:2575:4: warning: 'strncat' output may be truncated copying 99 bytes from a string of length 99 [-Wstringop-truncation]
strncat(ncg2, ncg, 99);
^~~~~~~~~~~~~~~~~~~~~~
gene-algorithms.c:2576:4: warning: 'strncpy' output may be truncated copying 99 bytes from a string of length 102 [-Wstringop-truncation]
strncpy(ncg, ncg2, 99);
^~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gene-value-index.c -o gene-value-index.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hashtable.c -o hashtable.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c index-builder.c -o index-builder.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-blc.c -o input-blc.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c input-files.c -o input-files.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c interval_merge.c -o interval_merge.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c long-hashtable.c -o long-hashtable.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c longread-mapping.c -o longread-mapping.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mergeVCF.c -o mergeVCF.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c processExons.c -o processExons.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c propmapped.c -o propmapped.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c qualityScores.c -o qualityScores.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read-repair.c -o read-repair.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c readSummary.c -o readSummary.o
readSummary.c: In function 'scRNA_merged_write_sparse_matrix':
readSummary.c:4412:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
fprintf(ofp_bcs,"%s\n", ArrayListGet(global_context -> scRNA_cell_barcodes_array, bc_no));
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%p
readSummary.c:4412:23: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=]
fprintf(ofp_bcs,"%s\n", ArrayListGet(global_context -> scRNA_cell_barcodes_array, bc_no));
~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%p
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum_WRT':
readSummary.c:4493:21: warning: pointer targets in initialization of 'char *' from 'unsigned char *' differ in signedness [-Wpointer-sign]
char * gene_name = global_context -> gene_name_array[ kyGeneID - NULL-1 ];
^~~~~~~~~~~~~~
readSummary.c:4489:11: warning: unused variable 'sample_no' [-Wunused-variable]
srInt_64 sample_no = me -> counter1;
^~~~~~~~~
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum':
readSummary.c:4502:11: warning: unused variable 'x1' [-Wunused-variable]
srInt_64 x1;
^~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids_WRT':
readSummary.c:4521:22: warning: pointer targets in initialization of 'char *' from 'unsigned char *' differ in signedness [-Wpointer-sign]
char* gene_symbol = global_context -> gene_name_array [k-NULL-1];
^~~~~~~~~~~~~~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids':
readSummary.c:4529:11: warning: unused variable 'x1' [-Wunused-variable]
srInt_64 x1;
^~
readSummary.c: In function 'scRNA_merged_45K_to_90K_sum':
readSummary.c:4506:31: warning: '.AmbSum' directive writing 7 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
sprintf(ofname,"%s.scRNA.%03d.AmbSum",global_context->input_file_name, sample_no+1);
^~~~~~~
readSummary.c:4506:2: note: 'sprintf' output between 18 and 1025 bytes into a destination of size 1020
sprintf(ofname,"%s.scRNA.%03d.AmbSum",global_context->input_file_name, sample_no+1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readSummary.c: In function 'scRNA_merged_write_nozero_geneids':
readSummary.c:4527:31: warning: '.no0Genes' directive writing 9 bytes into a region of size between 3 and 1010 [-Wformat-overflow=]
sprintf(ofname,"%s.scRNA.%03d.no0Genes",global_context->input_file_name, samplenno+1);
^~~~~~~~~
readSummary.c:4527:2: note: 'sprintf' output between 20 and 1027 bytes into a destination of size 1020
sprintf(ofname,"%s.scRNA.%03d.no0Genes",global_context->input_file_name, samplenno+1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c removeDupReads.c -o removeDupReads.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam2bed.c -o sam2bed.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sambam-file.c -o sambam-file.o
sambam-file.c: In function 'PBam_chunk_headers':
sambam-file.c:560:6: warning: 'strncpy' specified bound 100 equals destination size [-Wstringop-truncation]
strncpy(new_event->chro_name, chro_name, BAM_MAX_CHROMOSOME_NAME_LEN);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seek-zlib.c -o seek-zlib.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sorted-hashtable.c -o sorted-hashtable.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sublog.c -o sublog.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.1.2\"" -D_FILE_OFFSET_BITS=64 -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tx-unique.c -o tx-unique.o
/mingw64/bin/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 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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_2.1.2.zip
* DONE (Rsubread)