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 |
* 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.
* 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)