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Package 332/467HostnameOS / ArchBUILDCHECKBUILD BIN
pdInfoBuilder 1.16.0
Benilton Carvalho
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/pdInfoBuilder
Last Changed Rev: 54808 / Revision: 59457
Last Changed Date: 2011-04-13 18:03:42 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: pdInfoBuilder
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pdInfoBuilder_1.16.0.tar.gz
StartedAt: 2011-10-20 16:33:20 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 16:36:04 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 164.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: pdInfoBuilder.Rcheck
Warnings: 2

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/pdInfoBuilder.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'pdInfoBuilder' can be installed ... WARNING
Found the following significant warnings:
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
See '/Users/biocbuild/bbs-2.8-bioc/meat/pdInfoBuilder.Rcheck/00install.out' for details.
* checking installed package size ... 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 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
combinePgfClfProbesetsMps: no visible binding for global variable
  'ptype'
parseNgsTrio: no visible binding for global variable 'mismatch'
parseProbeSequenceFile: no visible binding for global variable 'count'
* 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 sizes of PDF files under inst/doc ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   howto-AffymetrixMapping.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, 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-4.2 -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-4.2 -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 oligoClasses version 1.14.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
================================================================================
Welcome to oligo version 1.16.2
================================================================================
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
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 1.16.2
================================================================================
Warning messages:
1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 

* DONE (pdInfoBuilder)

pdInfoBuilder.Rcheck/pdInfoBuilder-Ex.timings:

nameusersystemelapsed
AffyExpressionPDInfoPkgSeed-class0.0020.0010.002
AffySNPCNVPDInfoPkgSeed-class0.0010.0010.001
AffySNPCNVPDInfoPkgSeed2-class0.0020.0000.001
AffySNPPDInfoPkgSeed-class0.7100.0130.785
AffySNPPDInfoPkgSeed2-class0.0010.0000.001
AffySTPDInfoPkgSeed-class0.0010.0010.001
AffyTilingPDInfoPkgSeed-class0.0010.0000.002
NgsExpressionPDInfoPkgSeed-class0.0010.0000.001
NgsTilingPDInfoPkgSeed-class0.0010.0010.002
NimbleGenPDInfoPkgSeed-class0.0010.0000.001
makePdInfoPackage0.0010.0000.001