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Package 59/671HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.10.0
Mark Dunning
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/beadarray
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: beadarray
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarray_2.10.0.tar.gz
StartedAt: 2013-05-01 02:39:54 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 02:52:42 -0700 (Wed, 01 May 2013)
EllapsedTime: 768.5 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/beadarray.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 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '2.10.0'
* 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 'beadarray' can be installed ... [19s/20s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    2.6Mb
* 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 call with 'PACKAGE' argument in a different package:
  .Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
expressionQCPipeline: warning in ggsave(im, file = fname.im, width = 4,
  height = 1): partial argument match of 'file' to 'filename'
makeControlProfile: warning in packageDescription(annoPkg, field =
  "Version"): partial argument match of 'field' to 'fields'
plotMAXY: warning in close.screen(all = TRUE): partial argument match
  of 'all' to 'all.screens'
summarize: warning in packageDescription(annoPkg, field = "Version"):
  partial argument match of 'field' to 'fields'
combinedControlPlot: no visible binding for global variable 'Control'
combinedControlPlot: no visible binding for global variable 'Negative'
combinedControlPlot: no visible binding for global variable 'ID'
combinedControlPlot: no visible binding for global variable
  'Log2Intensity'
combinedControlPlot: no visible binding for global variable
  'ControlType'
combinedControlPlot: no visible binding for global variable 'Masked'
getPlatformSigs: no visible global function definition for
  'lumiHumanIDMapping_dbconn'
getPlatformSigs: no visible global function definition for
  'lumiMouseIDMapping_dbconn'
getPlatformSigs: no visible global function definition for
  'lumiRatIDMapping_dbconn'
imageplot: no visible binding for global variable 'Var1'
imageplot: no visible binding for global variable 'Var2'
imageplot: no visible binding for global variable 'value'
* 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 ... [551s/572s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 96.171  2.206  99.853
summarize                62.224  6.250  69.555
outlierplot              33.637  2.339  36.458
calculateOutlierStats    28.062  3.762  34.805
normaliseIllumina        23.778  3.727  28.315
addFeatureData           20.518  0.881  22.095
calculateDetection       17.570  3.425  21.948
controlProbeDetection    17.139  2.299  22.400
makeQCTable              16.478  2.876  19.628
insertSectionData        16.244  3.033  19.694
poscontPlot              15.974  1.874  18.237
showArrayMask            13.186  1.839  15.278
identifyControlBeads     13.890  1.049  15.821
quickSummary             12.872  1.682  14.752
imageplot                11.316  2.119  14.881
annotationInterface      12.053  1.035  13.405
combine                  10.550  1.979  14.088
boxplot                   8.403  2.060  10.859
illuminaOutlierMethod     5.820  1.145   8.128
transformationFunctions   5.687  1.228   7.034
plotMAXY                  5.519  1.199   7.229
plotBeadIntensities       5.399  0.884   6.422
insertBeadData            4.281  1.091   5.461
plotBeadLocations         4.287  0.718   5.148
* 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/beadarray.Rcheck/00check.log'
for details.

beadarray.Rcheck/00install.out:

* installing *source* package 'beadarray' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BASH.c -o BASH.o
BASH.c:81:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *margined = (int *) R_alloc(*no, sizeof(int));
                                ˜˜˜˜˜˜˜ ^˜˜
BASH.c:82:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *windowed = (int *) R_alloc(*no, sizeof(int));
                                ˜˜˜˜˜˜˜ ^˜˜
BASH.c:202:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *invaded = (int *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(int) ); //must be big enough to contain IDs of all invaded nodes 
                               ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:203:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *invadedE = (double *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(double));
                                      ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:204:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *done = (int *) R_alloc(*nbeads, sizeof(int));
                            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:206:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(done, 0, sizeof(int) * *nbeads);
                                    ˜ ^˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
BASH.c:206:39: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(done, 0, sizeof(int) * *nbeads);
                                    ˜ ^˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
BASH.c:306:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *invaded = (int *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(int) ); //must be big enough to contain IDs of all invaded nodes 
                               ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:307:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *invadedE = (double *) R_alloc(10 * (*invasions) * (*invasions + 1),  sizeof(double) );
                                      ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:308:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *invadedW = (double *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(double) );
                                      ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:310:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *done = (int *) R_alloc(*nbeads, sizeof(int));
                            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:312:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(done, 0, *nbeads * sizeof(int));
                        ^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
BASH.c:312:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(done, 0, *nbeads * sizeof(int));
                        ^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
BASH.c:441:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *done = (int *) R_alloc(*nbeads, sizeof(int));
                            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:442:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(done, 0, *nbeads * sizeof(int));
                        ^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
BASH.c:442:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(done, 0, *nbeads * sizeof(int));
                        ^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
BASH.c:445:56: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *choose = (double *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(double) );
                                    ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:446:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *thresh = (int *) R_alloc(10 * (*invasions) * (*invasions + 1), sizeof(int) );
                              ˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
BASH.c:470:33: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *outlier = (int *) R_alloc(*nbeads, sizeof(int));
                               ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:582:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *done = (int *) R_alloc(*nbeads, sizeof(int));
                            ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
BASH.c:583:44: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *marker = (int *) R_alloc((*invasions + 1), sizeof(int));
                              ˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜^˜˜
BASH.c:587:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(done, 0, *nbeads * sizeof(int));
                        ^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
BASH.c:587:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        memset(done, 0, *nbeads * sizeof(int));
                        ^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
23 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c HULK.c -o HULK.o
HULK.c:14:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  int *done = (int *) R_alloc(*nbeads, sizeof(int));
                      ˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
HULK.c:15:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(done, 0, *nbeads * sizeof(int));
                  ^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
HULK.c:15:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
  memset(done, 0, *nbeads * sizeof(int));
                  ^˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
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 determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c:105:20: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        tmpInt = 2 * pow(0, col % 2);
               ˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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 findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c:22:29: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        mid = floor((right-left)/2)+left;
            ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
findAllOutliers.c:88:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        tempArr = (double *) R_alloc(length, sizeof(double));
                             ˜˜˜˜˜˜˜ ^˜˜˜˜˜
findAllOutliers.c:95:6: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        i = floor(length/2);
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
findAllOutliers.c:111:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *arr2 = (double *) R_alloc(length, sizeof(double));
                                  ˜˜˜˜˜˜˜ ^˜˜˜˜˜
findAllOutliers.c:163:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        inten = (double *) R_alloc(*count, sizeof(double));
                           ˜˜˜˜˜˜˜ ^˜˜˜˜˜
findAllOutliers.c:192:25: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
                nsize1 = (sizeof(int) * (i+1));
                       ˜  ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
findAllOutliers.c:192:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                nsize1 = (sizeof(int) * (i+1));
                                      ˜  ˜^˜
findAllOutliers.c:193:41: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                validInds = (int *)realloc(validInds, nsize1);  
                                   ˜˜˜˜˜˜˜            ^˜˜˜˜˜
findAllOutliers.c:201:26: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
                        nsize1 = (sizeof(int) * (i+1));
                               ˜  ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
findAllOutliers.c:201:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        nsize1 = (sizeof(int) * (i+1));
                                              ˜  ˜^˜
findAllOutliers.c:202:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        validInds = (int *)realloc(validInds, nsize1);  
                                           ˜˜˜˜˜˜˜            ^˜˜˜˜˜
findAllOutliers.c:208:26: warning: implicit conversion changes signedness: 'unsigned long' to 'int' [-Wsign-conversion]
                        nsize2 = (sizeof(int) * (j+1));
                               ˜  ˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜
findAllOutliers.c:208:30: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
                        nsize2 = (sizeof(int) * (j+1));
                                              ˜  ˜^˜
findAllOutliers.c:209:46: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
                        outlierInds = (int *)realloc(outlierInds, nsize2);
                                             ˜˜˜˜˜˜˜              ^˜˜˜˜˜
14 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c imageProcessing.c -o imageProcessing.o
imageProcessing.c:43:38: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                        M[count++] = REAL(pixelMatrix)[tmp + k];
                                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
imageProcessing.c:88:13: warning: unknown pragma ignored [-Wunknown-pragmas]
    #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
            ^
imageProcessing.c:135:13: warning: unknown pragma ignored [-Wunknown-pragmas]
    #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
            ^
imageProcessing.c:244:13: warning: unknown pragma ignored [-Wunknown-pragmas]
    #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
            ^
imageProcessing.c:251:13: warning: unknown pragma ignored [-Wunknown-pragmas]
    #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
            ^
imageProcessing.c:282:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    for(i = x - 3.5; i <= x + 3.5; i++) {
          ˜ ˜˜^˜˜˜˜
imageProcessing.c:283:19: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        for(j = y - 3.5; j <= y + 3.5; j++) {
              ˜ ˜˜^˜˜˜˜
7 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 beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/beadarray.Rcheck/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (beadarray)

beadarray.Rcheck/beadarray-Ex.timings:

nameusersystemelapsed
BASH0.2260.0090.240
BASHCompact0.0100.0030.013
BASHDiffuse0.0110.0040.037
BASHExtended0.0120.0030.015
HULK0.0100.0030.015
addFeatureData20.518 0.88122.095
annotationInterface12.053 1.03513.405
backgroundCorrectSingleSection0.0050.0090.015
beadarrayUsersGuide0.0090.0070.016
boxplot 8.403 2.06010.859
calculateDetection17.570 3.42521.948
calculateOutlierStats28.062 3.76234.805
class-beadLevelData3.7520.5824.555
class-illuminaChannel0.0080.0060.014
combine10.550 1.97914.088
controlProbeDetection17.139 2.29922.400
createTargetsFile0.0020.0040.006
expressionQCPipeline0.0700.0110.096
generateNeighbours0.0040.0070.011
getBeadData3.7900.5944.553
identifyControlBeads13.890 1.04915.821
illuminaOutlierMethod5.8201.1458.128
imageplot11.316 2.11914.881
insertBeadData4.2811.0915.461
insertSectionData16.244 3.03319.694
makeControlProfile1.0220.1941.233
makeQCTable16.478 2.87619.628
medianNormalise3.1750.9074.132
metrics3.0110.3963.464
noOutlierMethod2.9570.3363.340
normaliseIllumina23.778 3.72728.315
numBeads3.9090.4534.534
outlierplot33.637 2.33936.458
plotBeadIntensities5.3990.8846.422
plotBeadLocations4.2870.7185.148
plotChipLayout0.0290.1250.157
plotMAXY5.5191.1997.229
poscontPlot15.974 1.87418.237
quickSummary12.872 1.68214.752
readBeadSummaryData0.0390.1030.142
sectionNames3.8610.4714.446
showArrayMask13.186 1.83915.278
squeezedVarOutlierMethod96.171 2.20699.853
summarize62.224 6.25069.555
transformationFunctions5.6871.2287.034
weightsOutlierMethod0.0040.0070.011