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BioC 2.14: CHECK report for BeadDataPackR on morelia

This page was generated on 2014-10-08 09:04:14 -0700 (Wed, 08 Oct 2014).

Package 72/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BeadDataPackR 1.16.0
Mike Smith
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/BeadDataPackR
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: BeadDataPackR
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BeadDataPackR_1.16.0.tar.gz
StartedAt: 2014-10-07 21:24:00 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:24:18 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 18.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BeadDataPackR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BeadDataPackR_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/BeadDataPackR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BeadDataPackR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BeadDataPackR’ version ‘1.16.0’
* 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 ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c BeadDataPackR.c -o BeadDataPackR.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -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 -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-2.14-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
compressBeadData0.0630.0040.067
decompressBeadData0.0410.0030.067
extractLocsFile0.0190.0010.021
readCompressedData0.0120.0020.013