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BioC 3.3: CHECK report for Rsubread on morelia

This page was generated on 2015-10-20 14:20:36 -0400 (Tue, 20 Oct 2015).

Package 919/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 1.21.0
Wei Shi
Snapshot Date: 2015-10-19 20:20:06 -0400 (Mon, 19 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread
Last Changed Rev: 109592 / Revision: 109765
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsubread
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rsubread_1.21.0.tar.gz
StartedAt: 2015-10-20 10:42:03 -0400 (Tue, 20 Oct 2015)
EndedAt: 2015-10-20 10:42:37 -0400 (Tue, 20 Oct 2015)
EllapsedTime: 34.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Rsubread.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rsubread_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsubread’ version ‘1.21.0’
* 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:
  .BBSoptions
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 ... [8s/8s] OK
* checking installed package size ... NOTE
  installed size is 22.3Mb
  sub-directories of 1Mb or more:
    annot  20.5Mb
* 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
createAnnotationFile: no visible global function definition for
  ‘values’
createAnnotationFile: no visible global function definition for
  ‘seqnames’
createAnnotationFile: no visible global function definition for
  ‘strand’
getInBuiltAnnotation: no visible binding for global variable
  ‘annot.inbuilt’
write.Rsubread: no visible global function definition for ‘values’
write.Rsubread: no visible global function definition for ‘seqnames’
write.Rsubread: no visible global function definition for ‘strand’
Undefined global functions or variables:
  annot.inbuilt seqnames strand values
* 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 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 compiled code ... NOTE
File ‘Rsubread/libs/Rsubread.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘SNPCalling.o’, ‘build-sam-index.o’, ‘core-indel.o’,
      ‘core-interface-aligner.o’, ‘core-interface-subjunc.o’, ‘core.o’,
      ‘input-files.o’, ‘propmapped.o’, ‘readSummary.o’,
      ‘sorted-hashtable.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘SNPCalling.o’, ‘core-indel.o’, ‘core.o’, ‘propmapped.o’
File ‘Rsubread/libs/Rsubread.so’:
  Found non-API call to R: ‘R_CStackLimit’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rsubread.Rcheck/00check.log’
for details.


Rsubread.Rcheck/00install.out:

* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Darwin.
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c HelperFunctions.c -o HelperFunctions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c R_wrapper.c -o R_wrapper.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c SNPCalling.c -o SNPCalling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c aligner.c -o aligner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c atgcContent.c -o atgcContent.o
atgcContent.c:71:7: warning: unused variable 'offset' [-Wunused-variable]
  int offset;
      ^
atgcContent.c:73:7: warning: unused variable 'data_ready' [-Wunused-variable]
  int data_ready=1;
      ^
atgcContent.c:70:7: warning: unused variable 'readlen' [-Wunused-variable]
  int readlen;
      ^
atgcContent.c:67:10: warning: unused variable 'len' [-Wunused-variable]
  size_t len = 0;
         ^
atgcContent.c:68:11: warning: unused variable 'z' [-Wunused-variable]
  ssize_t z;
          ^
atgcContent.c:108:10: warning: unused variable 'len' [-Wunused-variable]
  size_t len = 0;
         ^
atgcContent.c:109:11: warning: unused variable 'z' [-Wunused-variable]
  ssize_t z;
          ^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c build-sam-index.c -o build-sam-index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-bigtable.c -o core-bigtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-indel.c -o core-indel.o
core-indel.c:1743:28: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
                                if(head_indel_left_edge>=0 && abs(head_indel_movement)<=global_context -> config.max_indel_length)
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^ ˜
core-indel.c:2122:5: warning: variable 'all_reads' is uninitialized when used here [-Wuninitialized]
                                all_reads += 0xff&(next_moves>>(8*test_next));
                                ^˜˜˜˜˜˜˜˜
core-indel.c:2115:17: note: initialize the variable 'all_reads' to silence this warning
                        int all_reads;
                                     ^
                                      = 0
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-junction.c -o core-junction.o
core-junction.c:2993:170: warning: variable 'results' is uninitialized when used here [-Wuninitialized]
                newcore_extend_search_go(global_context, thread_context, read_name, read_text, scan_to_tail, candidate_last_base_in_exon_in_read, candidate_last_base_in_exon_on_chro, results, &found_events);
                                                                                                                                                                                       ^˜˜˜˜˜˜
core-junction.c:2978:16: note: initialize the variable 'results' to silence this warning
        void * results;
                      ^
                       = NULL
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core.c -o core.o
core.c:2491:25: warning: unused variable 'current_result' [-Wunused-variable]
                                                mapping_result_t *current_result = current_realignment_result -> mapping_result; 
                                                                  ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c detectionCall.c -o detectionCall.o
detectionCall.c:176:28: warning: unused variable 'read_entrezid' [-Wunused-variable]
        int read_start, read_end, read_entrezid, read_n, read_gc, read_at;
                                  ^
detectionCall.c:214:9: warning: unused variable 'z' [-Wunused-variable]
        size_t z;
               ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c:117:28: warning: unused variable 'read_length' [-Wunused-variable]
        int read_start, read_end, read_length;
                                  ^
detectionCallAnnotation.c:152:43: warning: unused variable 'read_length' [-Wunused-variable]
        int read_entrezid, read_start, read_end, read_length;
                                                 ^
detectionCallAnnotation.c:152:6: warning: unused variable 'read_entrezid' [-Wunused-variable]
        int read_entrezid, read_start, read_end, read_length;
            ^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c exon-align-indel.c -o exon-align-indel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c exon-align.c -o exon-align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c fullscan.c -o fullscan.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c fusion-align.c -o fusion-align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c gene-algorithms.c -o gene-algorithms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c gene-value-index.c -o gene-value-index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c hashtable.c -o hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c index-builder.c -o index-builder.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c input-files.c -o input-files.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c interval_merge.c -o interval_merge.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c long-hashtable.c -o long-hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c mergeVCF.c -o mergeVCF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c processExons.c -o processExons.o
processExons.c:237:10: warning: unused variable 'pt' [-Wunused-variable]
                        char *pt = strcpy(gene_array[gene_pos].chr_array[current_chr_index].id,chr_id);
                              ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c propmapped.c -o propmapped.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c qualityScores.c -o qualityScores.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c readSummary.c -o readSummary.o
readSummary.c:889:30: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
                        if(ret_features[xk1].start<0 || ret_features[xk1].start>0x7fffffff)
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
readSummary.c:896:28: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
                        if(ret_features[xk1].end<0 || ret_features[xk1].end>0x7fffffff)
                           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c removeDupReads.c -o removeDupReads.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c sam2bed.c -o sam2bed.o
sam2bed.c:43:7: warning: unused variable 'i' [-Wunused-variable]
  int i, readlen, chr_start, chr_end, flag, mqs;
      ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c sambam-file.c -o sambam-file.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c seek-zlib.c -o seek-zlib.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fPIC  -Wall -mtune=core2 -g -O2  -c sublog.c -o sublog.o
clang -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 R_wrapper.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 detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o fullscan.o fusion-align.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o long-hashtable.o mergeVCF.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.3-bioc/meat/Rsubread.Rcheck/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsubread)

Rsubread.Rcheck/Rsubread-Ex.timings:

nameusersystemelapsed
align1.7711.6483.421
buildindex0.4150.7601.185
createAnnotationFile0.0010.0000.001
featureCounts0.0010.0000.002
findCommonVariants000
getInBuiltAnnotation1.8540.0251.880
propmapped1.7371.2422.980
qualityScores0.0630.0020.067