Package: Biobase

Version: 2.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.20.0.tar.gz

StartedAt: 2013-05-01 02:48:32 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 02:51:20 -0700 (Wed, 01 May 2013)

EllapsedTime: 168.4 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Biobase.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 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '2.20.0'
* 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 'Biobase' can be installed ... [10s/10s] 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
cache: no visible binding for global variable 'cache_old'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
subListExtract 11.21  0.317  11.656
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [36s/37s]
  Running 'test-rowMedians.R' [31s/31s]
 [68s/68s] 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck/00check.log'
for details.

* installing *source* package 'Biobase' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c anyMissing.c -o anyMissing.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c envir.c -o envir.o
envir.c:21:61: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
      error("arg 'x' must be a 'list', not '%s'", type2char(TYPEOF(x)));
                                                  ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
envir.c:42:36: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
    PROTECT(nms = R_lsInternal(e1, all_nms));
                  ˜˜˜˜˜˜˜˜˜˜˜˜     ^˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
envir.c:61:23: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
            type2char(TYPEOF(x)));
            ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
envir.c:65:23: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
            type2char(TYPEOF(env)));
            ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
envir.c:119:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  rowData = (double *) R_alloc(ncol, sizeof(double));
                       ˜˜˜˜˜˜˜ ^˜˜˜
envir.c:179:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
            prefix[i] = toupper(first[i]);
                      ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
envir.c:185:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
                c = toupper(c);
                  ˜ ^˜˜˜˜˜˜˜˜˜
envir.c:162:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    min_nc = strlen(CHAR(STRING_ELT(x, 0)));
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
envir.c:167:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
        nc = strlen(CHAR(ans));
           ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c matchpt.c -o matchpt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c rowMedians.c -o rowMedians.o
rowMedians.c:31:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  rowData = (double *) R_alloc(ncol, sizeof(double));
                       ˜˜˜˜˜˜˜ ^˜˜˜
rowMedians.c:53:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  colOffset = (int *) R_alloc(ncol, sizeof(int));
                      ˜˜˜˜˜˜˜ ^˜˜˜
rowMedians.c:158:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  rowData = (int *) R_alloc(ncol, sizeof(int));
                    ˜˜˜˜˜˜˜ ^˜˜˜
rowMedians.c:179:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  colOffset = (int *) R_alloc(ncol, sizeof(int));
                      ˜˜˜˜˜˜˜ ^˜˜˜
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 sublist_extract.c -o sublist_extract.o
sublist_extract.c:28:25: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
              type2char(TYPEOF(v)));
              ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
sublist_extract.c:149:35: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
        PROTECT(ans = allocVector(TYPEOF(el), length(L)));
                      ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
sublist_extract.c:171:29: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
                  type2char(TYPEOF(el)));
                  ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
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 Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.029	0.003	0.032
ScalarObject-class	0.030	0.002	0.032
addVig2Menu	0.007	0.001	0.009
anyMissing	0.011	0.002	0.012
cache	0.018	0.003	0.022
channel	0.226	0.008	0.236
channelNames	0.067	0.002	0.070
class.AnnotatedDataFrame	0.085	0.007	0.094
class.ExpressionSet	0.610	0.033	0.663
class.MIAxE	0.051	0.001	0.053
class.MultiSet	0.114	0.003	0.121
class.NChannelSet	0.375	0.007	0.387
class.Versioned	0.157	0.005	0.169
class.VersionedBiobase	0.085	0.004	0.091
class.Versions	0.040	0.003	0.044
class.VersionsNull	0.010	0.001	0.011
class.container	0.011	0.001	0.013
class.eSet	0.219	0.011	0.235
classVersion	0.026	0.002	0.030
contents	0.010	0.001	0.012
copyEnv	0.010	0.001	0.011
copySubstitute	0.058	0.010	0.079
createPackage	0.034	0.005	0.044
data.aaMap	0.013	0.002	0.022
data.geneData	0.071	0.007	0.083
data.reporter	0.010	0.001	0.011
data.sample.ExpressionSet	0.029	0.007	0.036
data.sample.MultiSet	0.017	0.006	0.024
dumpPackTxt	0.012	0.002	0.028
esApply	2.526	0.042	2.601
getPkgVigs	0.065	0.013	0.131
isCurrent	0.093	0.004	0.097
isUnique	0.007	0.001	0.010
isVersioned	0.047	0.002	0.050
lcSuffix	0.128	0.003	0.133
listLen	0.010	0.000	0.011
makeDataPackage	0.123	0.012	0.136
matchpt	0.026	0.002	0.027
multiassign	0.021	0.002	0.023
note	0.007	0.001	0.007
openPDF	0.006	0.000	0.007
openVignette	0.009	0.001	0.010
package.version	0.007	0.001	0.007
read.AnnotatedDataFrame	0.029	0.003	0.032
read.MIAME	0.015	0.001	0.016
readExpressionSet	0.153	0.005	0.164
reverseSplit	0.016	0.000	0.016
rowMedians	0.129	0.008	0.138
rowQ	0.046	0.020	0.067
selectChannels	0.115	0.002	0.118
selectSome	0.006	0.003	0.010
strbreak	0.01	0.00	0.01
subListExtract	11.210	0.317	11.656
testBioCConnection	0.005	0.005	0.082
updateOldESet	0.003	0.002	0.005
validMsg	0.006	0.007	0.013