oligo 1.24.0
Benilton Carvalho
| 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/oligo | | 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/oligo.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 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking: 'doMC' 'doMPI'
* 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 'oligo' can be installed ... [22s/24s] OK
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
doc 2.6Mb
scripts 2.7Mb
* 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 ... NOTE
Foreign function calls with 'PACKAGE' argument in a different package:
.Call("ReadHeader", ..., PACKAGE = "affyio")
.Call("read_abatch", ..., PACKAGE = "affyio")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* 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 compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [152s/163s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
preprocessTools 50.919 3.205 56.480
getProbeInfo 33.404 2.475 41.634
fitProbeLevelModel 12.804 0.423 13.609
read.celfiles 8.716 1.194 10.376
basicPLM 5.624 0.028 5.825
basicRMA 5.602 0.026 5.851
rma-methods 4.840 0.166 5.234
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'doRUnit.R' [290s/536s]
[291s/538s] 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 were 3 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/oligo.Rcheck/00check.log'
for details.
* installing *source* package 'oligo' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c DABG.c -o DABG.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c:53:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
j = strlen(buffer)-1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ParserGzXYS.c:90:23: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
j = strlen(buffer)-1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c ParserXYS.c -o ParserXYS.o
ParserXYS.c:47:52: warning: implicit conversion changes signedness: 'long' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
while ((p = memchr(p, '\n', (buf + bytes_read) - p))) {
˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
ParserXYS.c:77:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
header->key = Realloc(header->key, header->n, char*);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
ParserXYS.c:78:50: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
header->value = Realloc(header->value, header->n, char*);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:63:68: note: expanded from macro 'Realloc'
#define Realloc(p,n,t) (t *) R_chk_realloc( (void *)(p), (size_t)((n) * sizeof(t)) )
^
ParserXYS.c:148:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
j = strlen(buffer)-1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
ParserXYS.c:189:14: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
xy[count] = strtol(sx, &endpx, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ParserXYS.c:190:21: warning: implicit conversion loses integer precision: 'long' to 'int' [-Wshorten-64-to-32]
xy[count + nrow] = strtol(sy, &endpy, 0);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ParserXYS.c:323:21: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
j = strlen(buffer)-1;
˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c baseProfile.c -o baseProfile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c basecontent.c -o basecontent.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c chipbackground.c -o chipbackground.o
chipbackground.c:379:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(data_by_sector[j],cur_n[j],sizeof(double),(int(*)(const void*, const void*))sort_double);
˜˜˜˜˜ ^˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mas5calls.c -o mas5calls.o
mas5calls.c:96:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
r = (double *) R_alloc(nx,sizeof(double));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:97:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
absx = (double *) R_alloc(nx,sizeof(double));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:98:28: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
xidx = (int *) R_alloc(nx,sizeof(int));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:104:30: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rsort_with_index(absx,xidx,nx);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
mas5calls.c:105:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rank(absx,nx,r);
˜˜˜˜ ^˜
mas5calls.c:151:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ignore = (int *) R_alloc(n, sizeof(int));
˜˜˜˜˜˜˜ ^
mas5calls.c:175:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
dv = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rma2.c -o rma2.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rma_common.c -o rma_common.o
rma_common.c:64:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
rma_common.c:64:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
rma_common.c:106:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
rma_common.c:106:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c trimmed.c -o trimmed.o
trimmed.c:29:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(buffer, n, sizeof(double), (int(*)(const void*, const void*))sort_double);
˜˜˜˜˜ ^
1 warning 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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/oligo.Rcheck/oligo/libs
** R
** inst
** preparing package for lazy loading
Note: in method for 'pm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for 'mm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligo)