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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1
Package 156/247HostnameOSArchBUILDCHECKBUILD BIN

oligo

1.1.13

Benilton Carvalho
Last Changed Date: 2007-08-20 20:55:00 -0700
Last Changed Rev: 26544
lamb1 Linux (SUSE 10.1) x86_64  TIMEOUT skipped
wellington Linux (SUSE 9.2) i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) x64  OK [ WARNINGS ] OK 
pitt Mac OS X (10.4.10) i386  OK  WARNINGS  OK 
Package: oligo
Version: 1.1.13
Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check oligo_1.1.13.tar.gz
RetCode: 0
Time: 327.2 seconds
Status: WARNINGS
CheckDir: oligo.Rcheck
Warnings: 3

Command output

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/oligo.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.1.13'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligo' can be installed ... WARNING
Found the following significant warnings:
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
       missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
See 'E:/biocbld/bbs-2.1-bioc/meat/oligo.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... 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 name space can be loaded with stated dependencies ... 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
justCRLMM: no visible binding for global variable 'maleIndex'
LLR2conf: no visible binding for global variable 'Dst'
LLR2conf: no visible binding for global variable 'HmzK3'
LLR2conf: no visible binding for global variable 'lm1'
LLR2conf: no visible binding for global variable 'HmzK2'
LLR2conf: no visible binding for global variable 'HtzK3'
LLR2conf: no visible binding for global variable 'lm2'
LLR2conf: no visible binding for global variable 'HtzK2'
LLR2conf: no visible binding for global variable 'SNRK'
LLR2conf: no visible binding for global variable 'SNRlm'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  justCRLMM justSNPRMA
Undocumented S4 classes:
  AffySNPCNVPDInfo SnpCnvFeatureSet SNPCNVPDInfo SnpCnvQSet
Undocumented S4 methods:
  generic 'boxplot' and siglist 'ExpressionSet'
  generic 'db' and siglist 'SnpCallSet'
  generic 'db' and siglist 'SnpCopyNumberSet'
  generic 'db' and siglist 'SnpQSet'
  generic 'db' and siglist 'SnpCnvQSet'
  generic 'db' and siglist 'SnpFeatureSet'
  generic 'featureNames' and siglist 'FeatureSet'
  generic 'getA' and siglist 'SnpCnvQSet'
  generic 'getM' and siglist 'SnpCnvQSet'
  generic 'hist' and siglist 'ExpressionSet'
  generic 'kind' and siglist 'AffySNPCNVPDInfo'
  generic 'pm' and siglist 'SnpCnvFeatureSet'
  generic 'pmindex' and siglist 'AffySNPCNVPDInfo'
  generic 'pmindex' and siglist 'SnpCnvFeatureSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'mmindex':
pmindex
  Code: function(object, ...)
  Docs: function(object)
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'mm':
pm
  Code: function(object, genenames = NULL, ...)
  Docs: function(object, genenames = NULL)
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'crlmm':
crlmm
  Code: function(object, correction = NULL, recalibrate = TRUE,
                 minLLRforCalls = c(5, 1, 5), verbose = TRUE,
                 correctionFile = NULL, prefix = "tmp.crlmm.", balance
                 = 1.5)
  Docs: function(object, correction = NULL, recalibrate = TRUE,
                 minPforCalls = c(0.5, 0.1, 0.5), verbose = TRUE,
                 correctionFile = NULL)
  Argument names in code not in docs:
    minLLRforCalls prefix balance
  Argument names in docs not in code:
    minPforCalls
  Mismatches in argument names:
    Position: 4 Code: minLLRforCalls Docs: minPforCalls

Codoc mismatches from documentation object 'read.celfiles':
read.celfiles
  Code: function(filenames, pkgname = NULL, phenoData =
                 new("AnnotatedDataFrame"), featureData = NULL,
                 description = NULL, notes = "", verbose = FALSE,
                 rm.mask = FALSE, rm.outliers = FALSE, rm.extra =
                 FALSE, tmpdir = getwd(), memory.bound = FALSE)
  Docs: function(filenames, pkgname = NULL, phenoData =
                 new("AnnotatedDataFrame"), featureData = NULL,
                 description = NULL, notes = "", verbose = FALSE,
                 rm.mask = FALSE, rm.outliers = FALSE, rm.extra =
                 FALSE, tmpdir = getwd())
  Argument names in code not in docs:
    memory.bound

Codoc mismatches from documentation object 'snprma':
snprma
  Code: function(object, verbose = TRUE, normalizeToHapmap = TRUE)
  Docs: function(oBatch, normalizeToHapmap = TRUE, saveQuant = FALSE)
  Argument names in code not in docs:
    object verbose
  Argument names in docs not in code:
    oBatch saveQuant
  Mismatches in argument names:
    Position: 1 Code: object Docs: oBatch
    Position: 2 Code: verbose Docs: normalizeToHapmap
    Position: 3 Code: normalizeToHapmap Docs: saveQuant

* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating oligo-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating oligo-manual.tex ... OK
* checking oligo-manual.tex ... OK

WARNING: There were 3 warnings, see
  E:/biocbld/bbs-2.1-bioc/meat/oligo.Rcheck/00check.log
for details

oligo.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/oligo.Rcheck


---------- Making package oligo ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making baseProfile.d from baseProfile.c
making basecontent.d from basecontent.c
making rma2.d from rma2.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
making trimmed.d from trimmed.c
gcc  -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include -I"e:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c baseProfile.c -o baseProfile.o
gcc  -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include -I"e:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c basecontent.c -o basecontent.o
gcc  -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include -I"e:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rma2.c -o rma2.o
gcc  -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include -I"e:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rma_background2.c -o rma_background2.o
gcc  -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include -I"e:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c rma_common.c -o rma_common.o
gcc  -Ie:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.1-bioc/R/include -I"e:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include" -Wall -O3 -std=gnu99   -c trimmed.c -o trimmed.o
windres -I e:/biocbld/bbs-2.1-bioc/R/include  -i oligo_res.rc -o oligo_res.o
gcc  -shared -s  -o oligo.dll oligo.def baseProfile.o basecontent.o rma2.o rma_background2.o rma_common.o trimmed.o oligo_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  preparing package oligo for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Loading required package: affyio
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: BufferedMatrix
Loading required package: BufferedMatrixMethods
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: affxparser
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'oligo'
     Formats: text html latex example chm 
  DBPDInfo-class                    text    html    latex   example chm
  FeatureSet-class                  text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  FeatureSetExtensions-class        text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  Index-methods                     text    html    latex   example chm
  IntensityMatrix-methods           text    html    latex   example chm
  PDInfo-class                      text    html    latex   example chm
  PDInfo-methods                    text    html    latex   example chm
  Sequences-methods                 text    html    latex   example chm
  SnpCallSet-methods                text    html    latex   example chm
  SnpCopyNumberSet-methods          text    html    latex   example chm
  SnpQSet-class                     text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  SnpQSet-methods                   text    html    latex   example chm
  SnpSetExtensions-class            text    html    latex   example chm
     missing link(s):  eSet-class VersionedBiobase-class Versioned-class eSet-class VersionedBiobase-class Versioned-class
  basecontent                       text    html    latex   example chm
  boxplot                           text    html    latex   example chm
  chromosome                        text    html    latex   example chm
  crlmm                             text    html    latex   example chm
  featureIndex                      text    html    latex   example chm
  genomeBuild                       text    html    latex   example chm
  getPlatformDesign                 text    html    latex   example chm
  hist                              text    html    latex   example chm
  image                             text    html    latex   example chm
  internals                         text    html    latex   example chm
  kind                              text    html    latex   example chm
  list.celfiles                     text    html    latex   example chm
  manufacturer                      text    html    latex   example chm
  nProbes                           text    html    latex   example chm
  ncol                              text    html    latex   example chm
  oligo-package                     text    html    latex   example chm
  platform                          text    html    latex   example chm
  platformDesign-class              text    html    latex   example chm
  plotDensity                       text    html    latex   example chm
  pmAllele                          text    html    latex   example chm
  pmPosition                        text    html    latex   example chm
  pmStrand                          text    html    latex   example chm
  probeNames                        text    html    latex   example chm
  read.celfiles                     text    html    latex   example chm
  read.xysfiles                     text    html    latex   example chm
  rma                               text    html    latex   example chm
  sequenceDesignMatrix              text    html    latex   example chm
  snprma                            text    html    latex   example chm
  snprmaSummaries                   text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm


Compile time: 0 minutes, 0 seconds
43	Topics
215	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\oligo.Rcheck\00_pkg_src\oligo\chm\oligo.chm, 41,634 bytes
Compression decreased file by 90,078 bytes.
  adding MD5 sums

* DONE (oligo)