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BioC 3.2: CHECK report for Rsubread on zin1

This page was generated on 2015-08-24 10:47:57 -0700 (Mon, 24 Aug 2015).

Package 892/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 1.19.3
Wei Shi
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread
Last Changed Rev: 106911 / Revision: 107696
Last Changed Date: 2015-07-29 20:19:39 -0700 (Wed, 29 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsubread
Version: 1.19.3
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rsubread_1.19.3.tar.gz
StartedAt: 2015-08-24 03:28:30 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 03:29:02 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 32.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Rsubread.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rsubread_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Rsubread.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.19.3’
* 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 ... [16s/16s] OK
* checking installed package size ... NOTE
  installed size is 23.6Mb
  sub-directories of 1Mb or more:
    annot  20.5Mb
    libs    1.8Mb
* 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 loading without being on the library search path ... 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’
* 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’, ‘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 ... [5s/5s] 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-3.2-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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c aligner.c -o aligner.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c atgcContent.c -o atgcContent.o
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:73:7: warning: unused variable ‘data_ready’ [-Wunused-variable]
   int data_ready=1;
       ^
atgcContent.c:71:7: warning: unused variable ‘offset’ [-Wunused-variable]
   int offset;
       ^
atgcContent.c:70:7: warning: unused variable ‘readlen’ [-Wunused-variable]
   int readlen;
       ^
atgcContent.c:68:11: warning: unused variable ‘z’ [-Wunused-variable]
   ssize_t z;
           ^
atgcContent.c:67:10: warning: unused variable ‘len’ [-Wunused-variable]
   size_t len = 0;
          ^
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:109:11: 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: 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);
         ^
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:111:7: warning: ‘readlen’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int readlen;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c build-sam-index.c -o build-sam-index.o
build-sam-index.c: In function ‘transfer_SAM_to_position_table’:
build-sam-index.c:363:47: warning: variable ‘is_anchor_certain’ set but not used [-Wunused-but-set-variable]
   int read_len, is_repeated, mapping_quality, is_anchor_certain=1;
                                               ^
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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c core-indel.c -o core-indel.o
core-indel.c: In function ‘find_new_indels’:
core-indel.c:1317:9: warning: variable ‘best_j’ set but not used [-Wunused-but-set-variable]
     int best_j=0, best_score=-99999, is_ambiguous_indel= 0;
         ^
core-indel.c: In function ‘full_indel_alignment’:
core-indel.c:2659:41: warning: variable ‘best_right’ set but not used [-Wunused-but-set-variable]
    int best_edge_score = -1, best_left, best_right;
                                         ^
core-indel.c:2659:30: warning: variable ‘best_left’ set but not used [-Wunused-but-set-variable]
    int best_edge_score = -1, best_left, best_right;
                              ^
core-indel.c: In function ‘find_potential_ultralong_indels’:
core-indel.c:2764:24: warning: variable ‘best_c2_location’ set but not used [-Wunused-but-set-variable]
   int best_match = -1, best_c2_location = -1;
                        ^
core-indel.c: In function ‘finalise_pileup_file’:
core-indel.c:3042:8: 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:3043:8: 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:3044:8: 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:3121:8: 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:3122:8: 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:3123:8: 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:3478:8: 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:3479:8: 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:3480:8: 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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c core-junction.c -o core-junction.o
core-junction.c: In function ‘search_events_to_back’:
core-junction.c:390:6: warning: variable ‘move_start’ set but not used [-Wunused-but-set-variable]
  int move_start = read_tail_pos - SEARCH_MIN_MOVEMENT;
      ^
core-junction.c: In function ‘finalise_explain_CIGAR’:
core-junction.c:1663:23: warning: variable ‘tmp_cigar_exonic’ set but not used [-Wunused-but-set-variable]
  char tmp_cigar[120], tmp_cigar_exonic[120];
                       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c core.c -o core.o
core.c: In function ‘print_in_box’:
core.c:89:7: warning: variable ‘is_R_linebreak’ set but not used [-Wunused-but-set-variable]
  char is_R_linebreak=0, * content, *out_line_buff;
       ^
core.c: In function ‘convert_GZ_to_FQ’:
core.c:759:19: warning: initialization from incompatible pointer type [enabled by default]
  gzFile * rawfp = gzopen(fname, "r");
                   ^
core.c:770:5: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [enabled by default]
     char * bufr =gzgets(rawfp, linebuff, 3000);
     ^
In file included from sambam-file.h:23:0,
                 from core.h:47,
                 from core.c:42:
/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:781:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
   gzclose(rawfp);
   ^
In file included from sambam-file.h:23:0,
                 from core.h:47,
                 from core.c:42:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
core.c: In function ‘do_voting’:
core.c:2979:9: warning: variable ‘allsubreads_for_each_gap’ set but not used [-Wunused-but-set-variable]
     int allsubreads_for_each_gap [GENE_SLIDING_STEP], noninformative_subreads_for_each_gap[GENE_SLIDING_STEP];
         ^
core.c: In function ‘split_read_files’:
core.c:3308:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
         ^
core.c:3310:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
          ^
core.c:3339:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
          ^
core.c:3340:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c detectionCall.c -o detectionCall.o
detectionCall.c: In function ‘build_ir_data_structure_map’:
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: In function ‘simplify_SAM_file’:
detectionCall.c:214:9: warning: unused variable ‘z’ [-Wunused-variable]
  size_t z;
         ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function ‘build_ir_data_structure’:
detectionCallAnnotation.c:117:28: warning: unused variable ‘read_length’ [-Wunused-variable]
  int read_start, read_end, read_length;
                            ^
detectionCallAnnotation.c: In function ‘breakIntegenicRegion’:
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;
      ^
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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c exon-align.c -o exon-align.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c fullscan.c -o fullscan.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c fusion-align.c -o fusion-align.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function ‘show_cigar’:
gene-algorithms.c:747:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable]
  int last_end=0, last_offset = 0, cursor = 0;
      ^
gene-algorithms.c:746:9: warning: variable ‘is_error’ set but not used [-Wunused-but-set-variable]
  int i, is_error = 0;
         ^
gene-algorithms.c: In function ‘match_chro_indel’:
gene-algorithms.c:1159:28: warning: variable ‘last_section_indels’ set but not used [-Wunused-but-set-variable]
  int last_section_end = 0, last_section_indels=0;
                            ^
gene-algorithms.c: In function ‘search_DP_branch’:
gene-algorithms.c:1703:6: warning: variable ‘table_mask2_j_1’ set but not used [-Wunused-but-set-variable]
  int table_mask2_j_1 = 0, table_mask2_i_1 = 0;
      ^
gene-algorithms.c: In function ‘final_mapping_quality’:
gene-algorithms.c:2344:7: warning: variable ‘is_match_begin’ set but not used [-Wunused-but-set-variable]
   int is_match_begin = 0;
       ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c gene-value-index.c -o gene-value-index.o
gene-value-index.c: In function ‘gvindex_load’:
gene-value-index.c:144:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
  int read_length;
      ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c index-builder.c -o index-builder.o
index-builder.c: In function ‘scan_gene_index’:
index-builder.c:449:19: warning: variable ‘table_no’ set but not used [-Wunused-but-set-variable]
  int file_number, table_no, i ,j;
                   ^
index-builder.c: In function ‘main_buildindex’:
index-builder.c:1123:9: 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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c input-files.c -o input-files.o
input-files.c: In function ‘geinput_next_char’:
input-files.c:442:10: 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 ‘sort_SAM_finalise’:
input-files.c:2188:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_name_len, 2,1 , bbfp);
          ^
input-files.c:2194:11: 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:2197:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_len,2,1,bbfp);
          ^
input-files.c:2203:11: 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:2256:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_name_len, 2,1 , bbfp);
          ^
input-files.c:2262:11: 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:2266:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&read_len, 2,1 , bbfp);
          ^
input-files.c:2269:11: 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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c interval_merge.c -o interval_merge.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c mergeVCF.c -o mergeVCF.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c processExons.c -o processExons.o
processExons.c: In function ‘find_chr’:
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);
          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c readSummary.c -o readSummary.o
readSummary.c: In function ‘readSummary’:
readSummary.c:3000:9: warning: variable ‘curchr_name’ set but not used [-Wunused-but-set-variable]
  char * curchr_name;
         ^
readSummary.c:2999:15: warning: variable ‘curpos’ set but not used [-Wunused-but-set-variable]
  long curchr, curpos;
               ^
readSummary.c:2999:7: warning: variable ‘curchr’ set but not used [-Wunused-but-set-variable]
  long curchr, curpos;
       ^
readSummary.c: In function ‘load_feature_info’:
readSummary.c:537:8: 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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c sam2bed.c -o sam2bed.o
sam2bed.c: In function ‘sam2bed’:
sam2bed.c:43:7: warning: unused variable ‘i’ [-Wunused-variable]
   int i, readlen, chr_start, chr_end, flag, mqs;
       ^
sam2bed.c:40:10: warning: variable ‘tok’ set but not used [-Wunused-but-set-variable]
   char * tok;
          ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c sambam-file.c -o sambam-file.o
sambam-file.c: In function ‘PBam_get_next_zchunk’:
sambam-file.c:324:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&ID1, 1, 1, bam_fp);
       ^
sambam-file.c:325:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&ID2, 1, 1, bam_fp);
       ^
sambam-file.c:326:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&CM, 1, 1, bam_fp);
       ^
sambam-file.c:327:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&FLG, 1, 1, bam_fp);
       ^
sambam-file.c:336:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&XLEN,1, 2, bam_fp );
       ^
sambam-file.c:344:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&SI1, 1, 1, bam_fp);
        ^
sambam-file.c:345:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&SI2, 1, 1, bam_fp);
        ^
sambam-file.c:346:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(&SLEN, 1, 2, bam_fp);
        ^
sambam-file.c:350:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
    fread(&BSIZE_MID, 1,2 , bam_fp);
         ^
sambam-file.c:362:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
   fread(buffer, 1, CDATA_READING, bam_fp);
        ^
sambam-file.c:366:8: 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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c: In function ‘load_int32’:
sorted-hashtable.c:1216:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
  int read_length;
      ^
sorted-hashtable.c: In function ‘load_int64’:
sorted-hashtable.c:1225:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
  int read_length;
      ^
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:1236:9: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
  int i, read_length;
         ^
sorted-hashtable.c:1249:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  fread(magic_chars,1,8,fp);
       ^
sorted-hashtable.c:1272:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&option_key, 2, 1, fp);
          ^
sorted-hashtable.c:1275:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
     fread(&option_length, 2, 1, fp);
          ^
sorted-hashtable.c:1278:11: 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-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.19.3\"" -fpic  -g -O2  -Wall -c sublog.c -o sublog.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-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-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 mergeVCF.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o sorted-hashtable.o sublog.o -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-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
align0.3391.0891.428
buildindex0.1680.3620.541
createAnnotationFile0.0000.0010.001
featureCounts0.0030.0000.001
findCommonVariants0.0000.0000.001
getInBuiltAnnotation1.4680.0111.478
propmapped0.3640.6881.053
qualityScores0.0590.0000.058