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Package 61/671HostnameOS / ArchBUILDCHECKBUILD BIN
BeadDataPackR 1.12.0
Mike Smith
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/BeadDataPackR
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: BeadDataPackR
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BeadDataPackR_1.12.0.tar.gz
StartedAt: 2013-05-01 02:42:31 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 02:42:54 -0700 (Wed, 01 May 2013)
EllapsedTime: 22.8 seconds
RetCode: 0
Status:  OK 
CheckDir: BeadDataPackR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BeadDataPackR.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 'BeadDataPackR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BeadDataPackR' version '1.12.0'
* 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 'BeadDataPackR' can be installed ... [2s/2s] 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
decompressBeadData: warning in readIntensities(con, nbead = nbeads):
  partial argument match of 'nbead' to 'nbeads'
decompressBeadData: warning in writeLocsFile(file = paste(outputPath,
  paste(outputMaskUsed, "_Grn.locs", sep = ""), sep =
  .Platform$file.sep), t(locs[, 1:2]), nBeads = header$nBeads): partial
  argument match of 'file' to 'fileName'
decompressBeadData: warning in writeLocsFile(file = paste(outputPath,
  paste(outputMaskUsed, "_Red.locs", sep = ""), sep =
  .Platform$file.sep), t(locs[, 3:4]), nBeads = header$nBeads): partial
  argument match of 'file' to 'fileName'
readCompressedData: warning in readIntensities(con, nbead = nbeads):
  partial argument match of 'nbead' to 'nbeads'
* 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 ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [1s/1s] 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/BeadDataPackR.Rcheck/00check.log'
for details.

BeadDataPackR.Rcheck/00install.out:

* installing *source* package 'BeadDataPackR' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c BeadDataPackR.c -o BeadDataPackR.o
BeadDataPackR.c:85:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(negResized, 0, sizeof(int) * nBytes * 4);
                                      ˜ ^˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
BeadDataPackR.c:85:41: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(negResized, 0, sizeof(int) * nBytes * 4);
                                      ˜ ^˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
BeadDataPackR.c:87:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(largeResized, 0, sizeof(int) * nBytes * 4);
                                        ˜ ^˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
   ? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest))     \
                                        ^
BeadDataPackR.c:87:43: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    memset(largeResized, 0, sizeof(int) * nBytes * 4);
                                        ˜ ^˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
   : __inline_memset_chk (dest, val, len))
                                     ^
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 R_init_BeadDataPackR.c -o R_init_BeadDataPackR.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o BeadDataPackR.so BeadDataPackR.o R_init_BeadDataPackR.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/BeadDataPackR.Rcheck/BeadDataPackR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BeadDataPackR)

BeadDataPackR.Rcheck/BeadDataPackR-Ex.timings:

nameusersystemelapsed
compressBeadData0.0940.0050.099
decompressBeadData0.0630.0070.075
extractLocsFile0.0290.0040.035
readCompressedData0.0200.0030.024