Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2021-12-07 12:34:02 -0500 (Tue, 07 Dec 2021).

CHECK results for Rsubread on merida1

To the developers/maintainers of the Rsubread package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1652/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.9.1  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2021-12-06 13:55:08 -0500 (Mon, 06 Dec 2021)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: master
git_last_commit: 0171e0c
git_last_commit_date: 2021-12-05 15:48:24 -0500 (Sun, 05 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Rsubread
Version: 2.9.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.9.1.tar.gz
StartedAt: 2021-12-07 04:24:53 -0500 (Tue, 07 Dec 2021)
EndedAt: 2021-12-07 04:31:06 -0500 (Tue, 07 Dec 2021)
EllapsedTime: 373.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rsubread.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.9.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsubread’ can be installed ... WARNING
Found the following significant warnings:
  cell-counts.c:1964:1: warning: control reaches end of non-void function [-Wreturn-type]
  cell-counts.c:2727:4: warning: "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) ==================" [-W#warnings]
                  #warning "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) =================="
  cell-counts.c:3987:20: warning: array index 1 is past the end of the array (which contains 1 element) [-Warray-bounds]
  cell-counts.c:4640:1: warning: control reaches end of non-void function [-Wreturn-type]
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 34.4Mb
  sub-directories of 1Mb or more:
    annot  28.5Mb
    libs    1.1Mb
    qualf   3.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.extract.sample.table.cols: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
propmapped 85.250  9.318  94.745
align      83.774  8.742  92.677
sublong    56.826  8.310  64.460
buildindex 24.277  5.323  29.725
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck/00check.log’
for details.



Installation output

Rsubread.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 2.9.1\""  -fPIC  -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -fPIC  -Wall -g -O2  -c R_wrapper.c -o R_wrapper.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 2.9.1\""  -fPIC  -Wall -g -O2  -c RsimReads.c -o RsimReads.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 2.9.1\""  -fPIC  -Wall -g -O2  -c SNPCalling.c -o SNPCalling.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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -fPIC  -Wall -g -O2  -c cell-counts.c -o cell-counts.o
cell-counts.c:1042:6: warning: unused variable 'curr_chro_number' [-Wunused-variable]
        int curr_chro_number = 0;
            ^
cell-counts.c:1409:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
        while(nch = *(cigar++)){
              ~~~~^~~~~~~~~~~~
cell-counts.c:1409:12: note: place parentheses around the assignment to silence this warning
        while(nch = *(cigar++)){
                  ^
              (               )
cell-counts.c:1409:12: note: use '==' to turn this assignment into an equality comparison
        while(nch = *(cigar++)){
                  ^
                  ==
cell-counts.c:1752:6: warning: unused variable 'x1' [-Wunused-variable]
        int x1=0;
            ^
cell-counts.c:1818:6: 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:1930:18: 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:1930:18: 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:1930:18: 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:1964:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
cell-counts.c:1969:30: warning: unused variable 'thread_context' [-Wunused-variable]
        cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                                    ^
cell-counts.c:2052:6: warning: unused variable 'lockret1' [-Wunused-variable]
        int lockret1=cellCounts_lock_occupy(&cct_context -> input_dataset_lock); 
            ^
cell-counts.c:2066:6: warning: unused variable 'lockret2' [-Wunused-variable]
        int lockret2=cellCounts_lock_release(&cct_context -> input_dataset_lock); 
            ^
cell-counts.c:2155:17: 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:2158:13: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(offsets[sri]!=0x77){
                          ^~~~
cell-counts.c:2159:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        *read_pos_move=offsets[sri];
                                              ^~~~
cell-counts.c:2167:13: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(offsets[sri]!=0x77){
                          ^~~~
cell-counts.c:2168:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        offsets[sri] -= (*read_pos_move);
                               ^~~~
cell-counts.c:2171:25: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                offset_cur = offsets[sri];
                                                    ^~~~
cell-counts.c:2173:29: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        high_conf_index = offsets[sri];
                                                 ^~~~
cell-counts.c:2175:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(offset_cur != offsets[sri] && subread0>0){
                                        ^~~~
cell-counts.c:2176:10: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        alnrec[toli]= subread0;
                              ^~~~~
cell-counts.c:2180:24: warning: array subscript is of type 'char' [-Wchar-subscripts]
                        offset_cur = offsets[sri];
                                            ^~~~
cell-counts.c:2188:13: warning: array subscript is of type 'char' [-Wchar-subscripts]
                if(offsets[sri]==0x77) subread0 =-1;
                          ^~~~
cell-counts.c:2191:11: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                alnrec[toli]= subread0;
                                      ^~~~~
cell-counts.c:2202:21: warning: array subscript is of type 'char' [-Wchar-subscripts]
                for(toli=0; alnrec[toli]; toli+=3){
                                  ^~~~~
cell-counts.c:2203:51: 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:2344:16: warning: unused variable 'meet_end' [-Wunused-variable]
                unsigned int meet_end = abs_pos + first_correct_base + indel_offset;
                             ^
cell-counts.c:2314:6: 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:2436:18: warning: unused variable 'topbuf' [-Wunused-variable]
        topK_buffer_t * topbuf = &thread_context->topKbuff;
                        ^
cell-counts.c:2599:7: 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:2727:4: warning: "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) ==================" [-W#warnings]
                #warning "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) =================="
                 ^
cell-counts.c:2721:7: 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:2859:6: warning: unused variable 'xk1' [-Wunused-variable]
        int xk1;
            ^
cell-counts.c:2865:6: warning: unused variable 'sqr_interval' [-Wunused-variable]
        int sqr_interval=10000;
            ^
cell-counts.c:2867:30: warning: unused variable 'thread_context' [-Wunused-variable]
        cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                                    ^
cell-counts.c:2879:15: warning: unused variable 'low_index_border' [-Wunused-variable]
        unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
                     ^
cell-counts.c:2880:15: 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:2970:6: warning: unused variable 'sqr_interval' [-Wunused-variable]
        int sqr_interval=10000;
            ^
cell-counts.c:2986:15: warning: unused variable 'low_index_border' [-Wunused-variable]
        unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
                     ^
cell-counts.c:2987:15: 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:3650:35: 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:3987:20: 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:3330:2: note: array 'inbin_batch_start_offsets' declared here
        int inbin_batch_start_offsets [CELLCOUNTS_BAMBLOCK_COMP_NUMBER ];
        ^
cell-counts.c:4111:14: warning: unused variable 'loaded_features' [-Wunused-variable]
        ArrayList * loaded_features = vp2[0];
                    ^
cell-counts.c:4112:14: 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:4147:14: 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:4640:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
43 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 2.9.1\""  -fPIC  -Wall -g -O2  -c core-bigtable.c -o core-bigtable.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 2.9.1\""  -fPIC  -Wall -g -O2  -c core-indel.c -o core-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 2.9.1\""  -fPIC  -Wall -g -O2  -c core-interface-aligner.c -o core-interface-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 2.9.1\""  -fPIC  -Wall -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.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 2.9.1\""  -fPIC  -Wall -g -O2  -c core-junction.c -o core-junction.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 2.9.1\""  -fPIC  -Wall -g -O2  -c core.c -o core.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 2.9.1\""  -fPIC  -Wall -g -O2  -c detection-calls.c -o detection-calls.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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -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 2.9.1\""  -fPIC  -Wall -g -O2  -c flattenAnnotations.c -o flattenAnnotations.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 2.9.1\""  -fPIC  -Wall -g -O2  -c fullscan.c -o fullscan.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 2.9.1\""  -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 2.9.1\""  -fPIC  -Wall -g -O2  -c gen_rand_reads.c -o gen_rand_reads.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 2.9.1\""  -fPIC  -Wall -g -O2  -c gene-algorithms.c -o gene-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 2.9.1\""  -fPIC  -Wall -g -O2  -c gene-value-index.c -o gene-value-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 2.9.1\""  -fPIC  -Wall -g -O2  -c hashtable.c -o 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 2.9.1\""  -fPIC  -Wall -g -O2  -c index-builder.c -o index-builder.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 2.9.1\""  -fPIC  -Wall -g -O2  -c input-blc.c -o input-blc.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 2.9.1\""  -fPIC  -Wall -g -O2  -c input-files.c -o input-files.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 2.9.1\""  -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 2.9.1\""  -fPIC  -Wall -g -O2  -c long-hashtable.c -o long-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 2.9.1\""  -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 2.9.1\""  -fPIC  -Wall -g -O2  -c mergeVCF.c -o mergeVCF.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 2.9.1\""  -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 2.9.1\""  -fPIC  -Wall -g -O2  -c propmapped.c -o propmapped.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 2.9.1\""  -fPIC  -Wall -g -O2  -c qualityScores.c -o qualityScores.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 2.9.1\""  -fPIC  -Wall -g -O2  -c read-repair.c -o read-repair.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 2.9.1\""  -fPIC  -Wall -g -O2  -c readSummary.c -o readSummary.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 2.9.1\""  -fPIC  -Wall -g -O2  -c removeDupReads.c -o removeDupReads.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 2.9.1\""  -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 2.9.1\""  -fPIC  -Wall -g -O2  -c sambam-file.c -o sambam-file.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 2.9.1\""  -fPIC  -Wall -g -O2  -c seek-zlib.c -o seek-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 2.9.1\""  -fPIC  -Wall -g -O2  -c sorted-hashtable.c -o sorted-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 2.9.1\""  -fPIC  -Wall -g -O2  -c sublog.c -o sublog.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 2.9.1\""  -fPIC  -Wall -g -O2  -c tx-unique.c -o tx-unique.o
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/4.2/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
** 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)

Tests output


Example timings

Rsubread.Rcheck/Rsubread-Ex.timings

nameusersystemelapsed
align83.774 8.74292.677
buildindex24.277 5.32329.725
featureCounts0.0000.0000.001
findCommonVariants000
getInBuiltAnnotation0.5490.0300.578
promoterRegions1.7710.0521.825
propmapped85.250 9.31894.745
qualityScores0.0650.0040.069
simReads0.0000.0000.001
sublong56.826 8.31064.460