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BioC 3.3: CHECK report for Rsubread on linux2.bioconductor.org

This page was generated on 2015-10-20 14:13:25 -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: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rsubread_1.21.0.tar.gz
StartedAt: 2015-10-20 07:43:49 -0400 (Tue, 20 Oct 2015)
EndedAt: 2015-10-20 07:44:26 -0400 (Tue, 20 Oct 2015)
EllapsedTime: 36.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Rsubread.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rsubread_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ... [18s/18s] OK
* checking installed package size ... NOTE
  installed size is 24.0Mb
  sub-directories of 1Mb or more:
    annot  20.5Mb
    libs    2.2Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/Rsubread.Rcheck/00check.log’
for details.

Rsubread.Rcheck/00install.out:

* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Linux.
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c HelperFunctions.c -o HelperFunctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c SNPCalling.c -o SNPCalling.o
SNPCalling.c: In function ‘read_tmp_block’:
SNPCalling.c:256:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(&SNP_rec, sizeof(SNP_rec),1 , tmp_fp);
         ^
SNPCalling.c:275:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(&read_rec, sizeof(read_rec), 1, tmp_fp);
         ^
SNPCalling.c:276:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(&read_len, sizeof(short), 1, tmp_fp);
         ^
SNPCalling.c:277:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(read, sizeof(char), read_len, tmp_fp);
         ^
SNPCalling.c:278:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(qual, sizeof(char), read_len, tmp_fp);
         ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c aligner.c -o aligner.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c atgcContent.c -o atgcContent.o
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:85:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets(line, MAX_LINE_LENGTH, fin);
         ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c build-sam-index.c -o build-sam-index.o
build-sam-index.c: In function ‘transform_pillup_to_index’:
build-sam-index.c:125:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&record, sizeof(record), 1, pile_fp);
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c core-bigtable.c -o core-bigtable.o
core-bigtable.c: In function ‘bigtable_readonly_result’:
core-bigtable.c:70:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(write_ptr, loadjunc?sizeof(subjunc_result_t):sizeof(mapping_result_t), 1,  global_context -> bigtable_cache_file_fp);
         ^
core-bigtable.c: In function ‘bigtable_retrieve_cache’:
core-bigtable.c:219:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread( current_cache -> big_margin_data , sizeof(short) * 3 * global_context -> config.big_margin_record_size , 1, global_context -> bigtable_cache_file_fp );
            ^
core-bigtable.c:220:12: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
       fread( current_cache -> alignment_res , sizeof(mapping_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp );
            ^
core-bigtable.c:223:14: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
         fread( current_cache -> subjunc_res , sizeof(subjunc_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp);
              ^
core-bigtable.c:229:14: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
     ftruncate(fileno(global_context -> bigtable_cache_file_fp), new_file_size);
              ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c core-indel.c -o core-indel.o
core-indel.c: In function ‘finalise_pileup_file’:
core-indel.c:3291:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&read_len, sizeof(short), 1, tmp_fp);
        ^
core-indel.c:3292:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(read_text, sizeof(char), read_len, tmp_fp);
        ^
core-indel.c:3293:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(qual_text, sizeof(char), read_len, tmp_fp);
        ^
core-indel.c:3370:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&read_len, sizeof(short), 1, tmp_fp);
        ^
core-indel.c:3371:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(read_text, sizeof(char), read_len, tmp_fp);
        ^
core-indel.c:3372:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(qual_text, sizeof(char), read_len, tmp_fp);
        ^
core-indel.c: In function ‘finalise_pileup_file_by_debrujin’:
core-indel.c:3734:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&read_len, sizeof(short), 1, tmp_fp);
        ^
core-indel.c:3735:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(read_text, sizeof(char), read_len, tmp_fp);
        ^
core-indel.c:3736:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(qual_text, sizeof(char), read_len, tmp_fp);
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c core-junction.c -o core-junction.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c core.c -o core.o
core.c: In function ‘convert_GZ_to_FQ’:
core.c:781:19: warning: initialization from incompatible pointer type [enabled by default]
  gzFile * rawfp = gzopen(fname, "r");
                   ^
core.c:792:5: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [enabled by default]
     char * bufr =gzgets(rawfp, linebuff, 3000);
     ^
In file included from subread.h:26:0,
                 from core.c:43:
/usr/include/zlib.h:1372:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                        ^
core.c:803:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
   gzclose(rawfp);
   ^
In file included from subread.h:26:0,
                 from core.c:43:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c detectionCall.c -o detectionCall.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function ‘calculateExonGCContent’:
detectionCallAnnotation.c:196:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, sizeof(line), fseq);
        ^
detectionCallAnnotation.c: In function ‘calculateIRGCContent’:
detectionCallAnnotation.c:283:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, sizeof(line), fseq);
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c exon-align-indel.c -o exon-align-indel.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c exon-align.c -o exon-align.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c fullscan.c -o fullscan.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c fusion-align.c -o fusion-align.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c gene-algorithms.c -o gene-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c gene-value-index.c -o gene-value-index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c index-builder.c -o index-builder.o
index-builder.c: In function ‘main_buildindex’:
index-builder.c:1166:9: warning: ignoring return value of ‘mkstemp’, declared with attribute warn_unused_result [-Wunused-result]
  mkstemp(tmp_fa_file);
         ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c input-files.c -o input-files.o
input-files.c: In function ‘geinput_next_char’:
input-files.c:503:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(out_buf, 1999,input->input_fp);
          ^
input-files.c: In function ‘SAM_pairer_writer_reset’:
input-files.c:2849:11: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
  ftruncate(fileno(bam_main -> bam_fp), 0);
           ^
input-files.c: In function ‘SAM_pairer_osr_next_name’:
input-files.c:2997:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&rlen, 1, 2, fp);
        ^
input-files.c:3009:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&rlen, 1, 2, fp);
        ^
input-files.c: In function ‘SAM_pairer_osr_next_bin’:
input-files.c:3019:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&rlen, 1, 2, fp);
       ^
input-files.c:3023:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&rlen, 1, 2, fp);
       ^
input-files.c:3026:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(bin, 1, rlen, fp);
       ^
input-files.c: In function ‘fix_load_next_block’:
input-files.c:3292:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(bam_buf, 1, bsize - xlen - 19, in);
         ^
input-files.c: In function ‘sort_SAM_finalise’:
input-files.c:3618:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_name_len, 2,1 , bbfp);
          ^
input-files.c:3624:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
      fread(read_name, 1, read_name_len, bbfp);
           ^
input-files.c:3627:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_len,2,1,bbfp);
          ^
input-files.c:3633:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
      fread(new_line_mem, 1, read_len, bbfp);
           ^
input-files.c:3686:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_name_len, 2,1 , bbfp);
          ^
input-files.c:3692:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
      fread(read_name_buf, 1, read_name_len, bbfp);
           ^
input-files.c:3696:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_len, 2,1 , bbfp);
          ^
input-files.c:3699:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
      fread(read_line_buf, 1, read_len, bbfp);
           ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c interval_merge.c -o interval_merge.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c long-hashtable.c -o long-hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c mergeVCF.c -o mergeVCF.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c processExons.c -o processExons.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c propmapped.c -o propmapped.o
propmapped.c: In function ‘prop_PE’:
propmapped.c:346:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
      fread(&read_len,1,1,fp);
           ^
propmapped.c:349:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
      fread(read_name,read_len,1,fp);
           ^
propmapped.c:353:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
      fread(&flags,1, sizeof(short), fp);
           ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c qualityScores.c -o qualityScores.o
qualityScores.c: In function ‘finalise_qs_context’:
qualityScores.c:82:4: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
    gzclose(qs_context -> gzfq_reader);
    ^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
qualityScores.c: In function ‘rewind_qs_file’:
qualityScores.c:275:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
   gzclose(qs_context -> gzfq_reader);
   ^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
qualityScores.c:282:29: warning: assignment from incompatible pointer type [enabled by default]
   qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
                             ^
qualityScores.c: In function ‘start_qs_context’:
qualityScores.c:313:29: warning: assignment from incompatible pointer type [enabled by default]
   qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
                             ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c readSummary.c -o readSummary.o
readSummary.c: In function ‘load_feature_info’:
readSummary.c:869:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(file_line, MAX_LINE_LENGTH, fp);
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c removeDupReads.c -o removeDupReads.o
removeDupReads.c: In function ‘parse_base_blocks’:
removeDupReads.c:87:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp);
          ^
removeDupReads.c:96:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp);
          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c sam2bed.c -o sam2bed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c sambam-file.c -o sambam-file.o
sambam-file.c: In function ‘PBam_get_next_zchunk’:
sambam-file.c:325:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&ID1, 1, 1, bam_fp);
       ^
sambam-file.c:326:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&ID2, 1, 1, bam_fp);
       ^
sambam-file.c:327:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&CM, 1, 1, bam_fp);
       ^
sambam-file.c:328:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&FLG, 1, 1, bam_fp);
       ^
sambam-file.c:337:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&XLEN,1, 2, bam_fp );
       ^
sambam-file.c:345:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&SI1, 1, 1, bam_fp);
        ^
sambam-file.c:346:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&SI2, 1, 1, bam_fp);
        ^
sambam-file.c:347:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&SLEN, 1, 2, bam_fp);
        ^
sambam-file.c:351:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(&BSIZE_MID, 1,2 , bam_fp);
         ^
sambam-file.c:363:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(buffer, 1, CDATA_READING, bam_fp);
        ^
sambam-file.c:367:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&real_len, 4, 1, bam_fp);
        ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c seek-zlib.c -o seek-zlib.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:1267:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(magic_chars,1,8,fp);
       ^
sorted-hashtable.c:1290:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&option_key, 2, 1, fp);
          ^
sorted-hashtable.c:1293:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&option_length, 2, 1, fp);
          ^
sorted-hashtable.c:1296:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
      fread(&(the_table -> index_gap),2,1,fp);
           ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic  -g -O2  -c sublog.c -o sublog.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/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 -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/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
align1.4971.5963.094
buildindex0.1970.0080.205
createAnnotationFile0.0000.0000.001
featureCounts0.0020.0000.001
findCommonVariants0.0000.0000.001
getInBuiltAnnotation1.2550.0001.253
propmapped1.5930.4072.001
qualityScores0.0790.0070.086