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Package 307/436HostnameOS / ArchBUILDCHECKBUILD BIN
pdInfoBuilder 1.15.2
Benilton Carvalho
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pdInfoBuilder
Last Changed Rev: 50555 / Revision: 53255
Last Changed Date: 2010-10-29 07:59:20 -0700 (Fri, 29 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK [ WARNINGS ] OK 

Summary

Package: pdInfoBuilder
Version: 1.15.2
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pdInfoBuilder_1.15.2.tar.gz
StartedAt: 2011-02-24 16:30:18 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 16:31:47 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 88.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: pdInfoBuilder.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pdInfoBuilder/DESCRIPTION' ... OK
* this is package 'pdInfoBuilder' version '1.15.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'pdInfoBuilder' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
combinePgfClfProbesetsMps: no visible binding for global variable
  'ptype'
parseNgsTrio: no visible binding for global variable 'mismatch'
parseProbeSequenceFile: no visible binding for global variable 'count'
makePdInfoPackage,NgsExpressionPDInfoPkgSeed: no visible binding for
  global variable 'ngsExprMmFeatureSchema'
makePdInfoPackage,NgsTilingPDInfoPkgSeed: no visible binding for global
  variable 'tiledRegionMmFeatureSchema'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'AffySNPPDInfoPkgSeed2-class':
Slots for class 'AffySNPPDInfoPkgSeed2'
  Code: author axiom biocViews cdfFile chipName csvAnnoFile csvSeqFile
        email genomebuild license manufacturer organism species url
        version
  Inherited: version license author email biocViews chipName
        manufacturer url genomebuild organism species
  Docs: author biocViews cdfFile chipName csvAnnoFile csvSeqFile email
        genomebuild license manufacturer organism species url version

* 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/pdInfoBuilder.Rcheck/00check.log'
for details

pdInfoBuilder.Rcheck/00install.out:

* installing *source* package 'pdInfoBuilder' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c pdInfoBuilder.c -o pdInfoBuilder.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pdInfoBuilder.so pdInfoBuilder.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/pdInfoBuilder.Rcheck/pdInfoBuilder/libs/i386
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: DBI
Loading required package: oligoClasses
================================================================================
Welcome to oligoClasses version 1.13.9
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
================================================================================
Welcome to oligo version 1.15.4
================================================================================
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (pdInfoBuilder)

pdInfoBuilder.Rcheck/pdInfoBuilder-Ex.timings:

nameusersystemelapsed
AffyExpressionPDInfoPkgSeed-class0.0010.0010.001
AffySNPCNVPDInfoPkgSeed-class0.0010.0000.001
AffySNPCNVPDInfoPkgSeed2-class0.0010.0000.002
AffySNPPDInfoPkgSeed-class0.5160.0080.523
AffySNPPDInfoPkgSeed2-class0.0010.0000.002
AffySTPDInfoPkgSeed-class0.0010.0000.002
AffyTilingPDInfoPkgSeed-class0.0010.0010.001
NgsExpressionPDInfoPkgSeed-class0.0010.0000.001
NgsTilingPDInfoPkgSeed-class0.0010.0010.001
NimbleGenPDInfoPkgSeed-class0.0010.0000.001
makePdInfoPackage0.0000.0010.001