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BioC 3.0: CHECK report for BufferedMatrixMethods on perceval

This page was generated on 2015-04-10 09:53:18 -0700 (Fri, 10 Apr 2015).

Package 116/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BufferedMatrixMethods 1.30.0
B. M. Bolstad
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BufferedMatrixMethods
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: BufferedMatrixMethods
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BufferedMatrixMethods_1.30.0.tar.gz
StartedAt: 2015-04-09 23:21:01 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:21:29 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 27.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BufferedMatrixMethods.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 BufferedMatrixMethods_1.30.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/BufferedMatrixMethods.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrixMethods/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BufferedMatrixMethods’ version ‘1.30.0’
* 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 ‘BufferedMatrixMethods’ can be installed ... [3s/4s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘affy’ ‘affyio’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘BufferedMatrix’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("read_probeintensities", ..., PACKAGE = "affyio")
  .Call("ReadHeader", ..., PACKAGE = "affyio")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

bg.correct.BufferedMatrix: no visible global function definition for
  ‘duplicate’
BufferedMatrix.bg.correct.normalize.quantiles: no visible global
  function definition for ‘duplicate’
BufferedMatrix.justRMA: no visible global function definition for
  ‘pData’
BufferedMatrix.justRMA: no visible global function definition for
  ‘read.celfile.header’
BufferedMatrix.justRMA: no visible global function definition for
  ‘cleancdfname’
BufferedMatrix.justRMA: no visible global function definition for
  ‘pmindex’
BufferedMatrix.justRMA: no visible global function definition for
  ‘geneNames’
BufferedMatrix.justRMA: no visible global function definition for
  ‘set.buffer.dim’
BufferedMatrix.justRMA: no visible global function definition for
  ‘RowMode’
BufferedMatrix.justRMA: no visible global function definition for
  ‘notes<-’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘createBufferedMatrix’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘read.celfile’
BufferedMatrix.read.celfiles: no visible global function definition for
  ‘AddColumn’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘cleancdfname’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘getCdfInfo’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘createBufferedMatrix’
BufferedMatrix.read.probematrix: no visible global function definition
  for ‘AddColumn’
normalize.BufferedMatrix.quantiles: no visible global function
  definition for ‘duplicate’
* 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 compiled code ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/BufferedMatrixMethods.Rcheck/00check.log’
for details.

BufferedMatrixMethods.Rcheck/00install.out:

* installing *source* package ‘BufferedMatrixMethods’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BufferedMatrix/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c init_package.c -o init_package.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BufferedMatrix/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c preprocess_bm.c -o preprocess_bm.o
preprocess_bm.c: In function ‘bm_rma_bg_correct’:
preprocess_bm.c:344: warning: unused variable ‘i’
preprocess_bm.c: In function ‘R_bm_rma_bg_correct’:
preprocess_bm.c:378: warning: unused variable ‘current_mode’
preprocess_bm.c: In function ‘R_bm_quantile_normalize’:
preprocess_bm.c:593: warning: unused variable ‘current_mode’
preprocess_bm.c: In function ‘R_bm_rma_bg_correct_quantile_normalize’:
preprocess_bm.c:1151: warning: unused variable ‘current_mode’
preprocess_bm.c: At top level:
preprocess_bm.c:453: warning: ‘min’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o BufferedMatrixMethods.so init_package.o preprocess_bm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/BufferedMatrixMethods.Rcheck/BufferedMatrixMethods/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BufferedMatrixMethods)