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Package 567/671HostnameOS / ArchBUILDCHECKBUILD BIN
rqubic 1.6.0
Jitao David Zhang
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/rqubic
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: rqubic
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rqubic_1.6.0.tar.gz
StartedAt: 2013-05-01 10:33:48 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 10:35:17 -0700 (Wed, 01 May 2013)
EllapsedTime: 89.6 seconds
RetCode: 0
Status:  OK 
CheckDir: rqubic.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rqubic.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rqubic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rqubic' version '1.6.0'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'rqubic' can be installed ... [7s/8s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... OK
* 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 for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'backup.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [13s/13s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
combineBiclusts-methods 5.262  0.063   5.381
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'c_output_parser_tests.R' [3s/3s]
  Running 'rqubic_implementations.R' [4s/5s]
  Running 'test_read.R' [2s/2s]
  Running 'test_utilities.R' [0s/1s]
 [11s/11s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/rqubic.Rcheck/00check.log'
for details.

rqubic.Rcheck/00install.out:

* installing *source* package 'rqubic' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c bicluster.c -o bicluster.o
bicluster.c:58:18: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int threshold = ceil(components * tolerance);
            ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bicluster.c:136:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(arr_rows, nrow);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:136:24: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(arr_rows, nrow);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:137:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(arr_rows_b, nrow); 
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:137:26: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(arr_rows_b, nrow); 
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:139:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(colcand, ncol);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:139:23: warning: implicit conversion changes signedness: 'const int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(colcand, ncol);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:160:23: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(arr_rows_b, nrow, sizeof *arr_rows, compare_int);
    ˜˜˜˜˜             ^˜˜˜
bicluster.c:201:28: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  int stackSize = (size+1) * sizeof(int);
      ˜˜˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
bicluster.c:201:24: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  int stackSize = (size+1) * sizeof(int);
                   ˜˜˜˜^˜  ˜
bicluster.c:202:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  struct dyStack *ds = malloc(stackSize);
                       ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
bicluster.c:230:13: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  qsort(el, n, sizeof *el, compare_block);
  ˜˜˜˜˜     ^
bicluster.c:278:20: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int btolerance = ceil(tolerance* block_rows);
      ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bicluster.c:339:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  int threshold = ceil(components * tolerance);
      ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bicluster.c:354:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
      if (flag=ss) (*m_cnt)++;
          ˜˜˜˜^˜˜
bicluster.c:354:15: note: place parentheses around the assignment to silence this warning
      if (flag=ss) (*m_cnt)++;
              ^
          (      )
bicluster.c:354:15: note: use '==' to turn this assignment into an equality comparison
      if (flag=ss) (*m_cnt)++;
              ^
              ==
bicluster.c:401:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(dexp, nrow);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:401:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(dexp, nrow);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:403:5: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
    AllocArray(dexp[i], ncol);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:403:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    AllocArray(dexp[i], ncol);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:413:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(symbols, sigma);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:413:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(symbols, sigma);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:430:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(bb, allocated); 
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:430:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(bb, allocated); 
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:438:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(profile, ncol);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:438:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(profile, ncol);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:439:30: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  for (j = 0; j < ncol; j++) AllocArray(profile[j], sigma);
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:439:53: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  for (j = 0; j < ncol; j++) AllocArray(profile[j], sigma);
                             ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:446:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(candidates, nrow);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:446:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(candidates, nrow);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:490:26: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    int cand_threshold = floor(mincol * tolerance);
        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bicluster.c:521:5: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
    AllocArray(colcand, ncol);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:521:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    AllocArray(colcand, ncol);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:531:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    int tol_cnt = floor(cnt * tolerance);
        ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
bicluster.c:610:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(output, n);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:610:22: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(output, n);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:621:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(blocks_rows_cnt, n);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:621:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(blocks_rows_cnt, n);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:622:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(blocks_cols_cnt, n);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:622:31: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(blocks_cols_cnt, n);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:623:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(blocks_rows, n);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:623:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(blocks_rows, n);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:624:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(blocks_cols, n);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:624:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(blocks_cols, n);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:652:7: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
      AllocArray(blocks_rows[j], blocks_rows_cnt[j]);
      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:652:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      AllocArray(blocks_rows[j], blocks_rows_cnt[j]);
      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
bicluster.c:653:7: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
      AllocArray(blocks_cols[j], blocks_cols_cnt[j]);
      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
bicluster.c:653:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
      AllocArray(blocks_cols[j], blocks_cols_cnt[j]);
      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
47 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c discretize.c -o discretize.o
discretize.c:16:22: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  const size_t lhs = (int)index;
               ˜˜˜   ^˜˜˜˜˜˜˜˜˜
discretize.c:45:59: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    if (cntl>0 && value<=quantile_from_sorted_data(downs, cntl, dspace * (i+1))) return -i-1;
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ^˜˜˜
discretize.c:46:57: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    if (cntu>0 && value>=quantile_from_sorted_data(ups, cntu,1.0-dspace*(i+1))) return i+1;
                         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜      ^˜˜˜
discretize.c:77:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ups, 0, ncol*sizeof(*ups));
                 ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
discretize.c:77:18: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(ups, 0, ncol*sizeof(*ups));
                 ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
discretize.c:78:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(downs, 0, ncol*sizeof(*downs));
                   ^˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
discretize.c:78:20: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(downs, 0, ncol*sizeof(*downs));
                   ^˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
discretize.c:86:20: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(rowdata, ncol, sizeof *rowdata, compare_continuous);
    ˜˜˜˜˜          ^˜˜˜
discretize.c:89:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    fhigh = quantile_from_sorted_data(rowdata, ncol, (1 - rq));
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
discretize.c:90:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    flow = quantile_from_sorted_data(rowdata, ncol, rq);
           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
discretize.c:91:47: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    fmed = quantile_from_sorted_data(rowdata, ncol, 0.5);
           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜          ^˜˜˜
In file included from discretize.c:9:
./rqubic.h:60:20: warning: unused variable 'EDGELIST_ATT_NAME' [-Wunused-variable]
static const char *EDGELIST_ATT_NAME="edgelist";
                   ^
./rqubic.h:61:20: warning: unused variable 'MINCOL_ATT_NAME' [-Wunused-variable]
static const char *MINCOL_ATT_NAME="minimumCol";
                   ^
13 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c fib.c -o fib.o
fib.c:83:7: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        oa = a;
           ˜ ^
fib.c:675:31: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                if ((h->fh_Dl = ceillog2(h->fh_n) + 1) < 8)
                                ˜˜˜˜˜˜˜˜ ˜˜˜^˜˜˜
fib.c:679:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                            sizeof *h->fh_cons * (h->fh_Dl + 1));
                                               ˜  ˜˜˜˜˜˜˜˜˜^˜˜
In file included from fib.c:35:
./rqubic.h:60:20: warning: unused variable 'EDGELIST_ATT_NAME' [-Wunused-variable]
static const char *EDGELIST_ATT_NAME="edgelist";
                   ^
./rqubic.h:61:20: warning: unused variable 'MINCOL_ATT_NAME' [-Wunused-variable]
static const char *MINCOL_ATT_NAME="minimumCol";
                   ^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c graph.c -o graph.o
graph.c:112:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  AllocArray(arr_c, nrow);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
graph.c:112:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  AllocArray(arr_c, nrow);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
graph.c:114:5: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
    AllocArray(arr_c[i], ncol);
    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:35:56: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                   ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
graph.c:114:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    AllocArray(arr_c[i], ncol);
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
./rqubic.h:35:59: note: expanded from macro 'AllocArray'
#define AllocArray(pt, size) (pt = xmalloc(sizeof(*pt) * (size)))
                                                          ^
graph.c:158:3: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
  ReAllocArray(edge_list, rec_num);
  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
./rqubic.h:36:63: note: expanded from macro 'ReAllocArray'
#define ReAllocArray(pt, size) (pt = xrealloc(pt, sizeof(*pt) * (size)))
                                     ˜˜˜˜˜˜˜˜     ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
graph.c:158:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  ReAllocArray(edge_list, rec_num);
  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
./rqubic.h:36:66: note: expanded from macro 'ReAllocArray'
#define ReAllocArray(pt, size) (pt = xrealloc(pt, sizeof(*pt) * (size)))
                                                                 ^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rqubic.c -o rqubic.o
rqubic.c:14:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  register void* value = malloc(size);
                         ˜˜˜˜˜˜ ^˜˜˜
rqubic.c:23:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  register void* value = realloc(ptr, size);
                         ˜˜˜˜˜˜˜      ^˜˜˜
In file included from rqubic.c:5:
./rqubic.h:60:20: warning: unused variable 'EDGELIST_ATT_NAME' [-Wunused-variable]
static const char *EDGELIST_ATT_NAME="edgelist";
                   ^
./rqubic.h:61:20: warning: unused variable 'MINCOL_ATT_NAME' [-Wunused-variable]
static const char *MINCOL_ATT_NAME="minimumCol";
                   ^
4 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o rqubic.so bicluster.o discretize.o fib.o graph.o rqubic.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rqubic.Rcheck/rqubic/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 (rqubic)

rqubic.Rcheck/rqubic-Ex.timings:

nameusersystemelapsed
QUBICBiclusterSet-class0.0120.0020.014
combineBiclusts-methods5.2620.0635.381
discretize0.0660.0120.078
eSetDimName0.1430.0120.156
fcFilter1.7160.0271.832
features-methods0.2620.0110.274
generateSeeds-methods0.2120.0100.221
parseQubicBlocks0.1960.0080.204
quBicluster1.6820.0261.717
readBiclusterResults0.0490.0080.102
writeQubicInputFile0.0850.0110.098