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This page was generated on 2021-09-18 12:06:53 -0400 (Sat, 18 Sep 2021).

INSTALL results for Rsubread on merida1

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raw results

Package 1623/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.7.3  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2021-09-17 14:50:09 -0400 (Fri, 17 Sep 2021)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: master
git_last_commit: d345cca
git_last_commit_date: 2021-09-10 01:05:57 -0400 (Fri, 10 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: Rsubread
Version: 2.7.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread
StartedAt: 2021-09-17 16:08:21 -0400 (Fri, 17 Sep 2021)
EndedAt: 2021-09-17 16:09:00 -0400 (Fri, 17 Sep 2021)
EllapsedTime: 39.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Darwin.
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.o
In file included from HelperFunctions.c:56:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from HelperFunctions.c:59:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c LRMbase-index.c -o LRMbase-index.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c LRMchro-event.c -o LRMchro-event.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c LRMfile-io.c -o LRMfile-io.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c LRMhashtable.c -o LRMhashtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c LRMhelper.c -o LRMhelper.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c LRMseek-zlib.c -o LRMseek-zlib.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c R_wrapper.c -o R_wrapper.o
In file included from R_wrapper.c:35:
In file included from ./HelperFunctions.h:24:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c RsimReads.c -o RsimReads.o
In file included from RsimReads.c:21:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c SNPCalling.c -o SNPCalling.o
In file included from SNPCalling.c:33:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from SNPCalling.c:36:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c aligner.c -o aligner.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c atgcContent.c -o atgcContent.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c build-sam-index.c -o build-sam-index.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c cell-counts.c -o cell-counts.o
In file included from cell-counts.c:9:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from cell-counts.c:10:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
cell-counts.c:714:26: warning: incompatible pointer types passing 'gene_value_index_t (*)[1]' to parameter of type 'gene_value_index_t *' [-Wincompatible-pointer-types]
        rv = rv || gvindex_load(&cct_context -> value_index, tmp_fname);
                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./gene-value-index.h:33:39: note: passing argument to parameter 'index' here
int gvindex_load(gene_value_index_t * index, const char filename []);
                                      ^
cell-counts.c:1033:6: warning: unused variable 'curr_chro_number' [-Wunused-variable]
        int curr_chro_number = 0;
            ^
cell-counts.c:1245:18: warning: incompatible pointer types passing 'gene_value_index_t (*)[1]' to parameter of type 'gene_value_index_t *' [-Wincompatible-pointer-types]
        gvindex_destory(&cct_context -> value_index);
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./gene-value-index.h:35:43: note: passing argument to parameter 'index' here
void gvindex_destory(gene_value_index_t * index);
                                          ^
cell-counts.c:1399:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
        while(nch = *(cigar++)){
              ~~~~^~~~~~~~~~~~
cell-counts.c:1399:12: note: place parentheses around the assignment to silence this warning
        while(nch = *(cigar++)){
                  ^
              (               )
cell-counts.c:1399:12: note: use '==' to turn this assignment into an equality comparison
        while(nch = *(cigar++)){
                  ^
                  ==
cell-counts.c:1762:2: warning: implicit declaration of function 'parallel_gzip_writer_add_text_qual' is invalid in C99 [-Wimplicit-function-declaration]
        parallel_gzip_writer_add_text_qual(outR1fp,R1qual, R1len,thread_no);
        ^
cell-counts.c:1738:6: warning: unused variable 'x1' [-Wunused-variable]
        int x1=0;
            ^
cell-counts.c:1804:6: warning: unused variable 'fields' [-Wunused-variable]
        int fields = cellCounts_scan_read_name_str(cct_context, NULL, read_name, &sample_seq, &sample_qual, &BC_seq, &BC_qual, &UMI_seq, &UMI_qual, &lane_str, &RG, &rname_trimmed_len);
            ^
cell-counts.c:1906:18: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
                for(nchi=0; nch= thread_context -> reporting_cigars[reporting_index][nchi]; nchi++){
                            ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:1906:18: note: place parentheses around the assignment to silence this warning
                for(nchi=0; nch= thread_context -> reporting_cigars[reporting_index][nchi]; nchi++){
                               ^
                            (                                                             )
cell-counts.c:1906:18: note: use '==' to turn this assignment into an equality comparison
                for(nchi=0; nch= thread_context -> reporting_cigars[reporting_index][nchi]; nchi++){
                               ^
                               ==
cell-counts.c:1940:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
cell-counts.c:1945:30: warning: unused variable 'thread_context' [-Wunused-variable]
        cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                                    ^
cell-counts.c:2120:17: warning: array subscript is of type 'char' [-Wchar-subscripts]
                for(sri=votrec[toli]; sri<=votrec[toli+1]; sri++) offsets[sri -1] = votrec[toli+2];
                              ^~~~~
cell-counts.c:2123:13: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(offsets[sri]!=0x77){
                          ^~~~
cell-counts.c:2124:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        *read_pos_move=offsets[sri];
                                              ^~~~
cell-counts.c:2132:13: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(offsets[sri]!=0x77){
                          ^~~~
cell-counts.c:2133:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        offsets[sri] -= (*read_pos_move);
                               ^~~~
cell-counts.c:2136:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                offset_cur = offsets[sri];
                                                    ^~~~
cell-counts.c:2138:29: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        high_conf_index = offsets[sri];
                                                 ^~~~
cell-counts.c:2140:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(offset_cur != offsets[sri] && subread0>0){
                                        ^~~~
cell-counts.c:2141:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        alnrec[toli]= subread0;
                              ^~~~~
cell-counts.c:2145:24: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        offset_cur = offsets[sri];
                                            ^~~~
cell-counts.c:2153:13: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(offsets[sri]==0x77) subread0 =-1;
                          ^~~~
cell-counts.c:2156:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                alnrec[toli]= subread0;
                                      ^~~~~
cell-counts.c:2167:21: warning: array subscript is of type 'char' [-Wchar-subscripts]
                for(toli=0; alnrec[toli]; toli+=3){
                                  ^~~~~
cell-counts.c:2168:51: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        SUBREADprintf("  %d ~ %d : indels=%d\n", alnrec[toli], alnrec[toli+1], alnrec[toli+2]);
                                                                       ^~~~~
cell-counts.c:2309:16: warning: unused variable 'meet_end' [-Wunused-variable]
                unsigned int meet_end = abs_pos + first_correct_base + indel_offset;
                             ^
cell-counts.c:2377:3: warning: "============ IMPROVE THIS FORMULA AS Subread ==========" [-W#warnings]
        #warning "============ IMPROVE THIS FORMULA AS Subread =========="
         ^
cell-counts.c:2279:6: warning: unused variable 'indels_in_highconf' [-Wunused-variable]
        int indels_in_highconf = cellCounts_indel_recorder_copy(indel_offsets, votetab -> indel_recorder[vote_i][vote_j], tolimax, all_subreads, &read_pos_move, read_name, abs_pos);
            ^
cell-counts.c:2404:18: warning: unused variable 'topbuf' [-Wunused-variable]
        topK_buffer_t * topbuf = &thread_context->topKbuff;
                        ^
cell-counts.c:2536:4: warning: "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) ==================" [-W#warnings]
                #warning "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) =================="
                 ^
cell-counts.c:2530:7: warning: unused variable 'subread_number_P1' [-Wunused-variable]
                int subread_number_P1 = 1+((myno >= applied_subreads_per_strand)?myno - applied_subreads_per_strand:myno);
                    ^
cell-counts.c:2621:6: warning: unused variable 'xk1' [-Wunused-variable]
        int xk1;
            ^
cell-counts.c:2627:6: warning: unused variable 'sqr_interval' [-Wunused-variable]
        int sqr_interval=10000;
            ^
cell-counts.c:2629:30: warning: unused variable 'thread_context' [-Wunused-variable]
        cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                                    ^
cell-counts.c:2641:15: warning: unused variable 'low_index_border' [-Wunused-variable]
        unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
                     ^
cell-counts.c:2642:15: warning: unused variable 'high_index_border' [-Wunused-variable]
        unsigned int high_index_border = cct_context -> value_index -> start_base_offset + cct_context -> value_index -> length; 
                     ^
cell-counts.c:3285:35: warning: assigning to 'Bytef *' (aka 'unsigned char *') from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
                        my_current_job -> strm.next_in = inbin_blk ;
                                                       ^ ~~~~~~~~~
cell-counts.c:3610:20: warning: array index 1 is past the end of the array (which contains 1 element) [-Warray-bounds]
                int nextoffset = finished_job -> task -> inbin_batch_start_offsets[1];
                                 ^                                                 ~
cell-counts.c:2964:2: note: array 'inbin_batch_start_offsets' declared here
        int inbin_batch_start_offsets [CELLCOUNTS_BAMBLOCK_COMP_NUMBER ];
        ^
cell-counts.c:3734:14: warning: unused variable 'loaded_features' [-Wunused-variable]
        ArrayList * loaded_features = vp2[0];
                    ^
cell-counts.c:3735:14: warning: unused variable 'sorted_order_p1_to_i_p1_tab' [-Wunused-variable]
        HashTable * sorted_order_p1_to_i_p1_tab = vp2[1];
                    ^
cell-counts.c:3770:14: warning: unused variable 'sorted_order_p1_to_i_p1_tab' [-Wunused-variable]
        HashTable * sorted_order_p1_to_i_p1_tab = tv2[1];
                    ^
cell-counts.c:4265:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
44 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c core-bigtable.c -o core-bigtable.o
In file included from core-bigtable.c:12:
In file included from ./core.h:46:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from core-bigtable.c:13:
In file included from ./core-bigtable.h:7:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c core-indel.c -o core-indel.o
In file included from core-indel.c:28:
In file included from ./HelperFunctions.h:24:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from core-indel.c:29:
In file included from ./gene-value-index.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
In file included from core-interface-aligner.c:7:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
In file included from core-interface-subjunc.c:7:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c core-junction.c -o core-junction.o
In file included from core-junction.c:25:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from core-junction.c:27:
In file included from ./gene-value-index.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c core.c -o core.o
In file included from core.c:45:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from core.c:50:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c detection-calls.c -o detection-calls.o
In file included from detection-calls.c:8:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from detection-calls.c:12:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c detectionCall.c -o detectionCall.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c exon-align-indel.c -o exon-align-indel.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c exon-align.c -o exon-align.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c flattenAnnotations.c -o flattenAnnotations.o
In file included from flattenAnnotations.c:41:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from flattenAnnotations.c:44:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c fullscan.c -o fullscan.o
In file included from fullscan.c:26:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from fullscan.c:27:
In file included from ./gene-value-index.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c fusion-align.c -o fusion-align.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c gen_rand_reads.c -o gen_rand_reads.o
In file included from gen_rand_reads.c:26:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from gen_rand_reads.c:31:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c gene-algorithms.c -o gene-algorithms.o
In file included from gene-algorithms.c:36:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from gene-algorithms.c:38:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c gene-value-index.c -o gene-value-index.o
In file included from gene-value-index.c:25:
In file included from ./gene-value-index.h:24:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from gene-value-index.c:25:
In file included from ./gene-value-index.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c hashtable.c -o hashtable.o
In file included from hashtable.c:18:
In file included from ./core.h:46:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c index-builder.c -o index-builder.o
In file included from index-builder.c:31:
In file included from ./gene-value-index.h:24:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from index-builder.c:31:
In file included from ./gene-value-index.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
index-builder.c:362:35: warning: result of comparison of constant 253 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                                if(next_char < 0 || next_char >= 253) {
                                                    ~~~~~~~~~ ^  ~~~
index-builder.c:365:39: warning: result of comparison of constant 255 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                                        if (next_char == -1 || next_char == 255) status = NEXT_READ;
                                                               ~~~~~~~~~ ^  ~~~
index-builder.c:366:39: warning: result of comparison of constant 254 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                                        if (next_char == -2 || next_char == 254) status = NEXT_FILE;
                                                               ~~~~~~~~~ ^  ~~~
index-builder.c:367:39: warning: result of comparison of constant 253 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                                        if (next_char == -3 || next_char == 253) return 0;
                                                               ~~~~~~~~~ ^  ~~~
index-builder.c:602:35: warning: result of comparison of constant 253 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                                if(next_char < 0 || next_char >= 253)
                                                    ~~~~~~~~~ ^  ~~~
index-builder.c:604:39: warning: result of comparison of constant 255 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                                        if (next_char == -1 || next_char == 255) status = NEXT_READ;
                                                               ~~~~~~~~~ ^  ~~~
index-builder.c:605:39: warning: result of comparison of constant 254 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                                        if (next_char == -2 || next_char == 254) status = NEXT_FILE;
                                                               ~~~~~~~~~ ^  ~~~
index-builder.c:606:39: warning: result of comparison of constant 253 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                                        if (next_char == -3 || next_char == 253) return 0;
                                                               ~~~~~~~~~ ^  ~~~
index-builder.c:1043:16: warning: result of comparison of constant 255 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                if(c==-1 || c==255) break;
                            ~^ ~~~
12 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c input-blc.c -o input-blc.o
In file included from input-blc.c:7:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from input-blc.c:10:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c input-files.c -o input-files.o
In file included from input-files.c:35:
In file included from ./input-files.h:23:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from input-files.c:41:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
input-files.c:276:37: warning: result of comparison of constant 255 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                        if(ch == '\n' || ch == EOF || ch == 255) break;
                                                      ~~ ^  ~~~
input-files.c:289:38: warning: result of comparison of constant 255 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                        if (ch == '\n' || ch == EOF || ch == 255) break;
                                                       ~~ ^  ~~~
input-files.c:552:23: warning: result of comparison of constant 255 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
                        if ((nch <0 || nch == 255) && feof((FILE *)input->input_fp))
                                       ~~~ ^  ~~~
6 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c interval_merge.c -o interval_merge.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c long-hashtable.c -o long-hashtable.o
In file included from long-hashtable.c:31:
In file included from ./core.h:46:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c longread-mapping.c -o longread-mapping.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c mergeVCF.c -o mergeVCF.o
In file included from mergeVCF.c:7:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from mergeVCF.c:10:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c processExons.c -o processExons.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c propmapped.c -o propmapped.o
In file included from propmapped.c:34:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from propmapped.c:39:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c qualityScores.c -o qualityScores.o
In file included from qualityScores.c:27:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c read-repair.c -o read-repair.o
In file included from read-repair.c:6:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c readSummary.c -o readSummary.o
In file included from readSummary.c:41:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from readSummary.c:44:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c removeDupReads.c -o removeDupReads.o
In file included from removeDupReads.c:27:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c sam2bed.c -o sam2bed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c sambam-file.c -o sambam-file.o
In file included from sambam-file.c:33:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from sambam-file.c:36:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
sambam-file.c:1930:9: warning: 'MAX_ALLOWED_GAP_IN_BAI_CHUNK' macro redefined [-Wmacro-redefined]
#define MAX_ALLOWED_GAP_IN_BAI_CHUNK 5 // the number of blocks, not the file positions.
        ^
./sambam-file.h:258:9: note: previous definition is here
#define MAX_ALLOWED_GAP_IN_BAI_CHUNK 10  // 10 blocks
        ^
4 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c seek-zlib.c -o seek-zlib.o
In file included from seek-zlib.c:2:
In file included from ./core.h:46:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from seek-zlib.c:5:
In file included from ./gene-algorithms.h:25:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
In file included from sorted-hashtable.c:20:
In file included from ./sorted-hashtable.h:25:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
In file included from sorted-hashtable.c:20:
./sorted-hashtable.h:31:2: warning: "REMOVE '- 69' NEXT LINE " [-W#warnings]
#warning "REMOVE '- 69' NEXT LINE "
 ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c sublog.c -o sublog.o
In file included from sublog.c:26:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fPIC  -Wall -g -O2  -c tx-unique.c -o tx-unique.o
In file included from tx-unique.c:6:
In file included from ./tx-unique.h:4:
./subread.h:205:2: warning: "============ ADD '-21' from next line  ================" [-W#warnings]
#warning "============ ADD '-21' from next line  ================"
 ^
./subread.h:207:2: warning: "============ ADD '-13' from next line  ================" [-W#warnings]
#warning "============ ADD '-13' from next line  ================"
 ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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
   ‘Rsubread.Rnw’ 
** 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)