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Package 450/671HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: oligo
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligo_1.24.0.tar.gz
StartedAt: 2013-05-01 08:44:46 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 09:00:23 -0700 (Wed, 01 May 2013)
EllapsedTime: 936.6 seconds
RetCode: 0
Status:  OK 
CheckDir: oligo.Rcheck
Warnings: 0

Command output

* 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.

oligo.Rcheck/00install.out:

* 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)

oligo.Rcheck/oligo-Ex.timings:

nameusersystemelapsed
Index-methods0.3020.0050.306
IntensityMatrix-methods3.4180.1374.075
MAplot-methods4.5210.1644.965
basecontent0.0020.0050.008
basicPLM5.6240.0285.825
basicRMA5.6020.0265.851
colors0.0650.0170.082
coordinates0.0030.0050.009
fitProbeLevelModel12.804 0.42313.609
getProbeInfo33.404 2.47541.634
image1.6220.1812.571
justSNPRMA0.0020.0060.008
list.xysfiles0.0020.0070.009
oligoPLM-class0.0050.0130.020
paCalls0.0040.0100.014
preprocessTools50.919 3.20556.480
read.celfiles 8.716 1.19410.376
read.xysfiles1.4150.2151.683
rma-methods4.8400.1665.234
sequenceDesignMatrix0.0260.0170.043