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Package 212/671HostnameOS / ArchBUILDCHECKBUILD BIN
externalVector 1.26.0
Bioconductor Package Maintainer
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/externalVector
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: externalVector
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch externalVector_1.26.0.tar.gz
StartedAt: 2013-05-01 05:09:22 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 05:10:41 -0700 (Wed, 01 May 2013)
EllapsedTime: 79.6 seconds
RetCode: 0
Status:  OK 
CheckDir: externalVector.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/externalVector.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 'externalVector/DESCRIPTION' ... OK
* this is package 'externalVector' version '1.26.0'
* 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 'externalVector' can be installed ... [13s/15s] 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
File 'externalVector/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(paste(msg, collapse = "\n"))
  .onAttach calls:
    library.dynam("externalVector", pkg, lib)

See section 'Good practice' in '?.onAttach'.

Arith,externalVectorWithStorage-missing: no visible binding for global
  variable '.generic'
Complex,externalVectorWithStorage: no visible binding for global
  variable 'x'
Subset2,ANY-ANY-noneIndex: possible error in Subset(x, i, NULL): unused
  argument (NULL)
Subset2,ANY-noneIndex-ANY: possible error in Subset(x, NULL, j): unused
  argument (j)
external.size,externalResource-gcAllocator: no visible binding for
  global variable 'x'
* 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/externalVector.Rcheck/externalVector/libs/externalVector.so':
  Found non-API calls to R: 'Rf_EncodeComplex', 'Rf_EncodeInteger',
    'Rf_EncodeLogical', 'Rf_EncodeReal', 'Rf_formatComplex',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... [3s/3s] OK
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/externalVector.Rcheck/00check.log'
for details.

externalVector.Rcheck/00install.out:

* installing *source* package 'externalVector' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c allocator.c -o allocator.o
allocator.c:29:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE mode = TYPEOF(type);
             ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
allocator.c:69:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    return allocVector(TYPEOF(store), 1);
           ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
allocator.c:97:29: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
            SEXPTYPE mode = TYPEOF(oldstore);
                     ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c arraySummary.c -o arraySummary.o
arraySummary.c:203:51: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                      asInteger(n), asInteger(p), asLogical(NaRm), COLSUM);
                                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
arraySummary.c:210:51: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                      asInteger(n), asInteger(p), asLogical(NaRm), COLMEAN);
                                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
arraySummary.c:217:51: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                      asInteger(n), asInteger(p), asLogical(NaRm), ROWSUM);
                                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
arraySummary.c:224:51: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                      asInteger(n), asInteger(p), asLogical(NaRm), ROWMEAN);
                                                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c coerce.c -o coerce.o
coerce.c:90:12: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    return x;
    ˜˜˜˜˜˜ ^
coerce.c:103:14: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    return x.r;
    ˜˜˜˜˜˜ ˜˜^
coerce.c:123:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                return xdouble;
                ˜˜˜˜˜˜ ^˜˜˜˜˜˜
coerce.c:213:11: warning: incompatible pointer types initializing 'char *' with an expression of type 'SEXP *' (aka 'struct SEXPREC **') [-Wincompatible-pointer-types]
    char *endp = STRING_PTR(x);
          ^      ˜˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c externalVector.c -o externalVector.o
externalVector.c:351:29: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                            asLogical(drop));
                            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
externalVector.c:353:24: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                       asLogical(drop));
                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
externalVector.c:826:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(ans, callDef, n*sizeof(R_CallMethodDef));
                         ^˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
externalVector.c:826:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(ans, callDef, n*sizeof(R_CallMethodDef));
                         ^˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
externalVector.c:839:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(ans, extDef, n*sizeof(R_ExternalMethodDef));
                        ^˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
externalVector.c:839:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(ans, extDef, n*sizeof(R_ExternalMethodDef));
                        ^˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
externalVector.c:914:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
               n[i]*sizeof(R_CallMethodDef));
               ^˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
externalVector.c:914:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
               n[i]*sizeof(R_CallMethodDef));
               ^˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
externalVector.c:918:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
           (n[0]+1)*sizeof(R_CallMethodDef));
            ˜˜˜˜^˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
externalVector.c:918:17: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
           (n[0]+1)*sizeof(R_CallMethodDef));
            ˜˜˜˜^˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
externalVector.c:927:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
               n_ext[i]*sizeof(R_ExternalMethodDef));
               ^˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
externalVector.c:927:16: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
               n_ext[i]*sizeof(R_ExternalMethodDef));
               ^˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
externalVector.c:931:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
           (n_ext[0]+1)*sizeof(R_ExternalMethodDef));
            ˜˜˜˜˜˜˜˜^˜ ˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
externalVector.c:931:21: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
           (n_ext[0]+1)*sizeof(R_ExternalMethodDef));
            ˜˜˜˜˜˜˜˜^˜ ˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
externalVector.c:6:1: warning: unused function 'ScalarVector' [-Wunused-function]
ScalarVector(SEXPTYPE mode, const primitiveElt_t* value)
^
15 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c groups.c -o groups.o
groups.c:12:12: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    return asLogical(ans);
    ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
groups.c:441:35: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        } else INTEGER(sAns)[0] = ans;
                                ˜ ^˜˜
groups.c:545:39: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
            } else INTEGER(sAns)[0] = ans;
                                    ˜ ^˜˜
groups.c:1708:36: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                    xelt.integer = myfmod(tmpx, tmpy);
                                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
groups.c:1723:37: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                else xelt.integer = floor((double) xelt.integer/
                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
groups.c:2094:28: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
        return allocVector(mode, 0);
               ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜
groups.c:2100:69: warning: operand of ? changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
                                       iop == POW_GENERIC))?REALSXP:mode);
                                                                    ^˜˜˜
groups.c:2150:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2160:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2170:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2180:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2190:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2200:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2234:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2244:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2254:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2264:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2274:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2284:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2319:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2331:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2373:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2384:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2395:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2406:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2417:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
groups.c:2428:32: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                xelt.logical = NA_LOGICAL;
                             ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
27 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c math.c -o math.o
math.c:154:30: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
        SEXPTYPE base_mode = TYPEOF(base);
                 ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c slice.c -o slice.o
slice.c:68:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memcpy(INTEGER(tmp), INTEGER(x), n*sizeof(int));
                                             ^˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
slice.c:68:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memcpy(INTEGER(tmp), INTEGER(x), n*sizeof(int));
                                             ^˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
slice.c:176:13: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    first = indx[0];
          ˜ ^˜˜˜˜˜˜
slice.c:181:23: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
            current = indx[i];
                    ˜ ^˜˜˜˜˜˜
slice.c:208:31: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                    current = indx[i];
                            ˜ ^˜˜˜˜˜˜
slice.c:234:31: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
                    current = indx[i];
                            ˜ ^˜˜˜˜˜˜
slice.c:308:40: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        stride = (double) (end - start)/(ns-1);
               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
slice.c:358:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE mode = TYPEOF((SEXP) s);
             ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
slice.c:391:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE mode = TYPEOF(s);
             ˜˜˜˜   ^˜˜˜˜˜˜˜˜
slice.c:421:40: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        stride = (double) (end - start)/(ns-1);
               ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
slice.c:592:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE mode = TYPEOF(x);
             ˜˜˜˜   ^˜˜˜˜˜˜˜˜
slice.c:667:21: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE mode = TYPEOF(x);
             ˜˜˜˜   ^˜˜˜˜˜˜˜˜
slice.c:835:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int start = content[0];
            ˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
slice.c:836:22: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        int stride = content[2];
            ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
slice.c:906:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        } else memcpy(ians, INTEGER(rowindx), nrow*sizeof(int));
                                              ^˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
slice.c:906:47: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        } else memcpy(ians, INTEGER(rowindx), nrow*sizeof(int));
                                              ^˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
16 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c storage.c -o storage.o
storage.c:77:22: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value->logical = LogicalFromInteger(value->integer, warn);
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:87:22: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value->logical = LogicalFromReal(value->numeric, warn);
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:97:22: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value->logical = LogicalFromComplex(value->cmplx, warn);
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:107:22: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value->logical = LogicalFromString(value->character, warn);
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:117:22: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value->logical = asLogical(value->any);
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
storage.c:451:23: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value1->logical = LogicalFromInteger(value->integer, warn);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:507:23: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value1->logical = LogicalFromReal(value->numeric, warn);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:563:23: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value1->logical = LogicalFromComplex(value->cmplx, warn);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:619:23: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value1->logical = LogicalFromString(value->character, warn);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:675:23: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    value1->logical = asLogical(value->any);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical               Rf_asLogical
                                ^
storage.c:1054:18: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    NA.logical = NA_LOGICAL;
               ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
storage.c:1508:18: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    NA.logical = NA_LOGICAL;
               ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
storage.c:1842:20: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    val->logical = LOGICAL((SEXP) x)[i];
                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:1949:9: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    n = strlen(nm);
      ˜ ^˜˜˜˜˜˜˜˜˜
storage.c:1982:13: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int n = strlen(nm);
        ˜   ^˜˜˜˜˜˜˜˜˜
storage.c:2527:34: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    logicalMethods->NA.logical = NA_LOGICAL;
                               ˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:51:20: note: expanded from macro 'NA_LOGICAL'
#define NA_LOGICAL      R_NaInt
                        ^˜˜˜˜˜˜
storage.c:2620:25: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
        SEXPTYPE mode = storageMethodsNameToMode(nm);
                 ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:2938:20: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    val->logical = ((int *) R_ExternalPtrAddr((SEXP) storage))[i];
                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
storage.c:3114:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(ans, R_CDef, n*sizeof(R_CMethodDef));
                        ^˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
   ? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest))     \
                                        ^
storage.c:3114:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memcpy(ans, R_CDef, n*sizeof(R_CMethodDef));
                        ^˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
   : __inline_memcpy_chk (dest, src, len))
                                     ^
20 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c subscript.c -o subscript.o
subscript.c:422:20: warning: incompatible pointer types assigning to 'StringEltGetter' (aka 'SEXP (*)(SEXP, int)') from 'SEXP (SEXP, R_xlen_t)' [-Wincompatible-pointer-types]
            getElt = STRING_ELT;
                   ^ ˜˜˜˜˜˜˜˜˜˜
subscript.c:464:16: warning: incompatible pointer types assigning to 'StringEltGetter' (aka 'SEXP (*)(SEXP, int)') from 'SEXP (SEXP, R_xlen_t)' [-Wincompatible-pointer-types]
        getElt = STRING_ELT; /* -Wall */
               ^ ˜˜˜˜˜˜˜˜˜˜
subscript.c:478:28: warning: incompatible pointer types assigning to 'StringEltGetter' (aka 'SEXP (*)(SEXP, int)') from 'SEXP (SEXP, R_xlen_t)' [-Wincompatible-pointer-types]
                    getElt = STRING_ELT;
                           ^ ˜˜˜˜˜˜˜˜˜˜
3 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 externalVector.so allocator.o arraySummary.o coerce.o externalVector.o groups.o math.o slice.o storage.o subscript.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/externalVector.Rcheck/externalVector/libs
** R
** preparing package for lazy loading
Creating a new generic function for 'setNames' in package 'externalVector'
Creating a generic function for 'match' from package 'base' in package 'externalVector'
Creating a generic function for 'as.vector' from package 'base' in package 'externalVector'
Creating a generic function for 'as.single' from package 'base' in package 'externalVector'
Creating a generic function for 'as.list' from package 'base' in package 'externalVector'
Creating a generic function for 'as.matrix' from package 'base' in package 'externalVector'
Creating a generic function for 'as.data.frame' from package 'base' in package 'externalVector'
Creating a generic function for 'colSums' from package 'base' in package 'externalVector'
Creating a generic function for 'colMeans' from package 'base' in package 'externalVector'
Creating a generic function for 'rowSums' from package 'base' in package 'externalVector'
Creating a generic function for 'rowMeans' from package 'base' in package 'externalVector'
Creating a generic function for 'apply' from package 'base' in package 'externalVector'
Creating a generic function for 'lapply' from package 'base' in package 'externalVector'
Creating a generic function for 'sapply' from package 'base' in package 'externalVector'
Creating a generic function for 'mean' from package 'base' in package 'externalVector'
Creating a generic function for 'median' from package 'stats' in package 'externalVector'
Creating a new generic function for 'var' in package 'externalVector'
Creating a new generic function for 'cov' in package 'externalVector'
Creating a new generic function for 'cor' in package 'externalVector'
Creating a generic function for 'cov2cor' from package 'stats' in package 'externalVector'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (externalVector)

externalVector.Rcheck/externalVector-Ex.timings:

nameusersystemelapsed
SubscriptList0.0140.0030.017
allNA0.0180.0020.026
as.Rvector0.0120.0020.015
asEach0.0610.0060.077
defaultElement0.0070.0010.008
externalMatrix0.0270.0030.046
externalVector0.0310.0030.060
gcAllocator-class0.0730.0070.090
makeSlice0.0090.0020.012
setExternalStorageClass0.0140.0010.017
setVirtualMethod0.0440.0030.051
var0.0360.0030.039