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Package 410/671HostnameOS / ArchBUILDCHECKBUILD BIN
mgsa 1.8.1
Sebastian Bauer
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/mgsa
Last Changed Rev: 75543 / Revision: 76155
Last Changed Date: 2013-04-10 16:47:11 -0700 (Wed, 10 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: mgsa
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mgsa_1.8.1.tar.gz
StartedAt: 2013-05-01 07:58:29 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 07:59:46 -0700 (Wed, 01 May 2013)
EllapsedTime: 77.0 seconds
RetCode: 0
Status:  OK 
CheckDir: mgsa.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/mgsa.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 'mgsa/DESCRIPTION' ... OK
* this is package 'mgsa' version '1.8.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'mgsa' can be installed ... [5s/6s] 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 ... NOTE
NB: .Last.lib will not be used unless it is exported
File 'mgsa/R/zzz.R':
  .Last.lib calls:
    library.dynam.unload("mgsa", paste(.libPaths(), "/mgsa", sep = ""))

Package detach functions should not call 'library.dynam.unload'.
See section 'Good practice' in '?.Last.lib'.

readGAF: no visible binding for global variable 'aspect.code'
readGAF: no visible binding for global variable 'evidence.code'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/mgsa.Rcheck/mgsa/libs/mgsa.so':
  Found '_printf', possibly from 'printf' (C)
    Object: 'mgsa.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mgsa-methods 12.853  0.040  13.013
readGAF       7.923  0.319   8.388
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/mgsa.Rcheck/00check.log'
for details.

mgsa.Rcheck/00install.out:

* installing *source* package 'mgsa' ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mgsa.c -o mgsa.o
mgsa.c:57:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp critical
        ^
mgsa.c:117:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (!(p->values = R_alloc(p->number_of_states,sizeof(p->values[0]))))
                                  ˜˜˜˜˜˜˜ ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:213:34: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                sample->u.discrete_index = rnd * prior->number_of_states;
                                         ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:268:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(sum->values = R_alloc(number_of_breaks,sizeof(sum->values[0]))))
                            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:270:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(sum->values,0,number_of_breaks * sizeof(sum->values[0]));
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mgsa.c:270:23: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(sum->values,0,number_of_breaks * sizeof(sum->values[0]));
                             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mgsa.c:271:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(sum->breaks = R_alloc(number_of_breaks,sizeof(sum->breaks[0]))))
                            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:323:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (!(sum->dmap = R_alloc(number_of_discrete_values,sizeof(sum->dmap[0]))))
                                  ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:376:68: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
                if (!(new_sum->breaks = (double*)R_alloc(1,sizeof(sum->breaks[0])*num_of_discrete_values)))
                                                 ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:376:69: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                if (!(new_sum->breaks = (double*)R_alloc(1,sizeof(sum->breaks[0])*num_of_discrete_values)))
                                                                                 ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:378:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(new_sum->breaks,sum->breaks,sizeof(sum->breaks[0])*num_of_discrete_values);
                                                                         ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
mgsa.c:378:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(new_sum->breaks,sum->breaks,sizeof(sum->breaks[0])*num_of_discrete_values);
                                                                         ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
mgsa.c:383:65: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
                if (!(new_sum->values = (int*)R_alloc(1,sizeof(sum->values[0])*num_of_discrete_values)))
                                              ˜˜˜˜˜˜˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:383:66: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                if (!(new_sum->values = (int*)R_alloc(1,sizeof(sum->values[0])*num_of_discrete_values)))
                                                                              ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:385:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(new_sum->values,sum->values,sizeof(sum->values[0])*num_of_discrete_values);
                                                                         ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
mgsa.c:385:61: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(new_sum->values,sum->values,sizeof(sum->values[0])*num_of_discrete_values);
                                                                         ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
mgsa.c:390:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (!(new_sum->dmap = R_alloc(num_of_discrete_values,sizeof(sum->dmap[0]))))
                                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:392:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(new_sum->dmap,sum->dmap,sizeof(sum->dmap[0])*num_of_discrete_values);
                                                                   ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
mgsa.c:392:55: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                memcpy(new_sum->dmap,sum->dmap,sizeof(sum->dmap[0])*num_of_discrete_values);
                                                                   ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
mgsa.c:414:49: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                slot = val * (sum->num_of_discrete_values -1) / (sum->pdsc->uniform_continous_upper - sum->pdsc->uniform_continous_lower);
                     ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:579:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(cn->sets_active = (int*)R_alloc(number_of_sets,sizeof(cn->sets_active[0]))))
                                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:581:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(cn->sets_active,0,number_of_sets * sizeof(cn->sets_active[0]));
                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mgsa.c:581:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(cn->sets_active,0,number_of_sets * sizeof(cn->sets_active[0]));
                                 ^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mgsa.c:582:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(cn->set_partition = (int*)R_alloc(number_of_sets,sizeof(cn->set_partition[0]))))
                                        ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:584:57: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(cn->position_of_set_in_partition = (int*)R_alloc(number_of_sets,sizeof(cn->position_of_set_in_partition[0]))))
                                                       ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:593:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(cn->hidden_count = (int*)R_alloc(n,sizeof(cn->hidden_count[0]))))
                                       ˜˜˜˜˜˜˜ ^
mgsa.c:595:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(cn->hidden_count,0,n * sizeof(cn->hidden_count[0]));
                                  ^ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mgsa.c:595:28: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(cn->hidden_count,0,n * sizeof(cn->hidden_count[0]));
                                  ^ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mgsa.c:597:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(cn->observable = (int*)R_alloc(n,sizeof(cn->observable[0]))))
                                     ˜˜˜˜˜˜˜ ^
mgsa.c:599:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(cn->observable,0,n * sizeof(cn->observable[0]));
                                ^ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mgsa.c:599:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(cn->observable,0,n * sizeof(cn->observable[0]));
                                ^ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mgsa.c:603:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(cn->max_score_sets_active = (int*)R_alloc(number_of_sets,sizeof(cn->max_score_sets_active[0]))))
                                                ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:607:54: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(cn->sets_activity_count = (uint64_t *)R_alloc(number_of_sets,sizeof(cn->sets_activity_count[0]))))
                                                    ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:609:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(cn->sets_activity_count,0,number_of_sets * sizeof(cn->sets_activity_count[0]));
                                         ^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
mgsa.c:609:35: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(cn->sets_activity_count,0,number_of_sets * sizeof(cn->sets_activity_count[0]));
                                         ^˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
mgsa.c:863:28: warning: implicit conversion changes signedness: 'int' to 'uint64_t' (aka 'unsigned long long') [-Wsign-conversion]
        return cn->number_of_sets + cn->number_of_inactive_sets * (cn->number_of_sets - cn->number_of_inactive_sets);
        ˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:900:23: warning: implicit conversion turns floating-point number into integer: 'double' to 'uint32_t' (aka 'unsigned int') [-Wconversion]
                uint32_t proposal = (double)(genrand(mt) * possibilities);
                         ˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:905:26: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        cn->proposal_toggle = proposal;
                                            ˜ ^˜˜˜˜˜˜˜
mgsa.c:906:20: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
                        toggle_state(cn,proposal);
                        ˜˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜˜
mgsa.c:912:20: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        proposal -= cn->number_of_sets;
                                 ˜˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:914:43: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        active_term_pos = (int)(proposal / cn->number_of_inactive_sets) +  cn->number_of_inactive_sets;
                                                         ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:915:45: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
                        inactive_term_pos = (int)(proposal % cn->number_of_inactive_sets);
                                                           ˜ ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:1141:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(res.marg_set_activity = (double*)R_alloc(number_of_sets,sizeof(res.marg_set_activity[0]))))
                                               ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
mgsa.c:1247:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(no =  (int*)R_alloc(lo,sizeof(no[0])))) /* R's garbage collection takes care of it */
                          ˜˜˜˜˜˜˜ ^˜
mgsa.c:1264:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(lset = (int*)R_alloc(lsets,sizeof(lset[0]))))
                           ˜˜˜˜˜˜˜ ^˜˜˜˜
mgsa.c:1266:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        if (!(nsets = (int**)R_alloc(lsets,sizeof(nsets[0]))))
                             ˜˜˜˜˜˜˜ ^˜˜˜˜
mgsa.c:1277:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (!(nsets[i] = (int*)R_alloc(lset[i],sizeof(nsets[i][0]))))
                                       ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
mgsa.c:1301:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                nas = R_alloc(las,sizeof(nas[0]));
                      ˜˜˜˜˜˜˜ ^˜˜
mgsa.c:1410:37: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                if (!(r = (struct result*)R_alloc(irestarts,sizeof(*r))))
                                          ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
mgsa.c:1432:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp parallel for
        ^
mgsa.c:1438:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma omp critical
        ^
mgsa.c:1440:25: warning: implicit conversion turns floating-point number into integer: 'double' to 'unsigned long' [-Wconversion]
                                seed = (unif_rand() * (double)(INT32_MAX));
                                     ˜  ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
52 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 mgsa.so mgsa.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/mgsa.Rcheck/mgsa/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'mgsa'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mgsa)

mgsa.Rcheck/mgsa-Ex.timings:

nameusersystemelapsed
MgsaSets-class0.0210.0010.022
mgsa-methods12.853 0.04013.013
readGAF7.9230.3198.388