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HTDA log file (check_x86_64_linux)

Sat Jun 14 00:15:19 2014: Checking package HTDA (SVN revision 59) ...
* using log directory ‘/mnt/building/build_2014-06-14-00-12/RF_PKG_CHECK/PKGS/HTDA.Rcheck’
* using R version 3.1.0 Patched (2014-06-12 r65926)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘HTDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTDA’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Who to complain to ’
New submission
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTDA’ can be installed ... [1s/1s] OK
* checking installed package size ... NOTE
  installed size is 14.5Mb
  sub-directories of 1Mb or more:
    extdata  14.3Mb
* 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘CAMERA’ ‘GOstats’ ‘GenomicRanges’ ‘PROcess’ ‘Rsamtools’ ‘amap’
  ‘limma’ ‘xcms’
'library' or 'require' calls not declared from:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘PROcess’
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DenovoAsmAnnoT: no visible binding for global variable ‘cpu’
QualityDenovo: no visible binding for global variable ‘file1’
QualityDenovo: no visible binding for global variable ‘file2’
QualityDenovo: no visible binding for global variable ‘seqtype’
SeqAna: no visible binding for global variable ‘db’
gcProcess: no visible binding for global variable ‘phenodata1’
rmBaseline: no visible global function definition for ‘read.files’
rnaseqProcess : gtf2GRangesList: no visible global function definition
  for ‘GRanges’
rnaseqProcess : gtf2GRangesList: no visible global function definition
  for ‘IRanges’
rnaseqProcess: no visible global function definition for ‘assays’
rnaseqProcess : returnRPKM: no visible global function definition for
  ‘width’
rnaseqProcess: no visible binding for global variable ‘phenodata’
* checking Rd files ... WARNING
prepare_Rd: AverageScan.Rd:19-21: Dropping empty section \details
prepare_Rd: AverageScan.Rd:36-38: Dropping empty section \note
prepare_Rd: AverageScan.Rd:33-35: Dropping empty section \author
prepare_Rd: AverageScan.Rd:30-32: Dropping empty section \references
prepare_Rd: AverageScan.Rd:42-44: Dropping empty section \seealso
prepare_Rd: DenovoAsmAnnoT.Rd:7-9: Dropping empty section \description
prepare_Rd: DenovoAsmAnnoT.Rd:40-42: Dropping empty section \details
prepare_Rd: DenovoAsmAnnoT.Rd:43-49: Dropping empty section \value
prepare_Rd: DenovoAsmAnnoT.Rd:56-58: Dropping empty section \note
prepare_Rd: DenovoAsmAnnoT.Rd:53-55: Dropping empty section \author
prepare_Rd: DenovoAsmAnnoT.Rd:50-52: Dropping empty section \references
prepare_Rd: DenovoAsmAnnoT.Rd:62-64: Dropping empty section \seealso
checkRd: (5) DenovoAsmAnnoT.Rd:0-114: Must have a \description
prepare_Rd: FinalTable.Rd:7-9: Dropping empty section \description
prepare_Rd: FinalTable.Rd:19-21: Dropping empty section \details
prepare_Rd: FinalTable.Rd:22-28: Dropping empty section \value
prepare_Rd: FinalTable.Rd:35-37: Dropping empty section \note
prepare_Rd: FinalTable.Rd:32-34: Dropping empty section \author
prepare_Rd: FinalTable.Rd:29-31: Dropping empty section \references
prepare_Rd: FinalTable.Rd:41-43: Dropping empty section \seealso
checkRd: (5) FinalTable.Rd:0-64: Must have a \description
prepare_Rd: HTDA-package.Rd:43-44: Dropping empty section \seealso
prepare_Rd: HTDA-package.Rd:45-46: Dropping empty section \examples
prepare_Rd: IndiMsScan.Rd:38-40: Dropping empty section \note
prepare_Rd: IndiMsScan.Rd:35-37: Dropping empty section \author
prepare_Rd: IndiMsScan.Rd:32-34: Dropping empty section \references
prepare_Rd: IndiMsScan.Rd:44-46: Dropping empty section \seealso
prepare_Rd: MultiVariAnalysis.Rd:7-9: Dropping empty section \description
prepare_Rd: MultiVariAnalysis.Rd:26-28: Dropping empty section \details
prepare_Rd: MultiVariAnalysis.Rd:29-35: Dropping empty section \value
prepare_Rd: MultiVariAnalysis.Rd:42-44: Dropping empty section \note
prepare_Rd: MultiVariAnalysis.Rd:39-41: Dropping empty section \author
prepare_Rd: MultiVariAnalysis.Rd:36-38: Dropping empty section \references
prepare_Rd: MultiVariAnalysis.Rd:48-50: Dropping empty section \seealso
checkRd: (5) MultiVariAnalysis.Rd:0-85: Must have a \description
prepare_Rd: NcmsProcessData-class.Rd:8-10: Dropping empty section \description
prepare_Rd: NcmsProcessData-class.Rd:37-39: Dropping empty section \note
prepare_Rd: NcmsProcessData-class.Rd:34-36: Dropping empty section \author
prepare_Rd: NcmsProcessData-class.Rd:31-33: Dropping empty section \references
prepare_Rd: NcmsProcessData-class.Rd:43-46: Dropping empty section \seealso
checkRd: (5) NcmsProcessData-class.Rd:0-51: Must have a \description
prepare_Rd: Parse.Rd:7-9: Dropping empty section \description
prepare_Rd: Parse.Rd:19-21: Dropping empty section \details
prepare_Rd: Parse.Rd:22-28: Dropping empty section \value
prepare_Rd: Parse.Rd:35-37: Dropping empty section \note
prepare_Rd: Parse.Rd:32-34: Dropping empty section \author
prepare_Rd: Parse.Rd:29-31: Dropping empty section \references
prepare_Rd: Parse.Rd:41-43: Dropping empty section \seealso
checkRd: (5) Parse.Rd:0-141: Must have a \description
prepare_Rd: PlotChrom.Rd:7-9: Dropping empty section \description
prepare_Rd: PlotChrom.Rd:19-21: Dropping empty section \details
prepare_Rd: PlotChrom.Rd:22-28: Dropping empty section \value
prepare_Rd: PlotChrom.Rd:35-37: Dropping empty section \note
prepare_Rd: PlotChrom.Rd:32-34: Dropping empty section \author
prepare_Rd: PlotChrom.Rd:29-31: Dropping empty section \references
prepare_Rd: PlotChrom.Rd:41-43: Dropping empty section \seealso
checkRd: (5) PlotChrom.Rd:0-61: Must have a \description
prepare_Rd: PreProcessData-class.Rd:8-10: Dropping empty section \description
prepare_Rd: PreProcessData-class.Rd:35-37: Dropping empty section \note
prepare_Rd: PreProcessData-class.Rd:32-34: Dropping empty section \author
prepare_Rd: PreProcessData-class.Rd:29-31: Dropping empty section \references
prepare_Rd: PreProcessData-class.Rd:41-44: Dropping empty section \seealso
checkRd: (5) PreProcessData-class.Rd:0-49: Must have a \description
prepare_Rd: QualityDenovo.Rd:30-32: Dropping empty section \details
prepare_Rd: QualityDenovo.Rd:33-39: Dropping empty section \value
prepare_Rd: QualityDenovo.Rd:46-48: Dropping empty section \note
prepare_Rd: QualityDenovo.Rd:43-45: Dropping empty section \author
prepare_Rd: QualityDenovo.Rd:40-42: Dropping empty section \references
prepare_Rd: QualityDenovo.Rd:52-54: Dropping empty section \seealso
prepare_Rd: SeqAna.Rd:31-33: Dropping empty section \details
prepare_Rd: SeqAna.Rd:34-40: Dropping empty section \value
prepare_Rd: SeqAna.Rd:47-49: Dropping empty section \note
prepare_Rd: SeqAna.Rd:44-46: Dropping empty section \author
prepare_Rd: SeqAna.Rd:41-43: Dropping empty section \references
prepare_Rd: SeqAna.Rd:53-55: Dropping empty section \seealso
prepare_Rd: SequnecAnalysisData-class.Rd:8-10: Dropping empty section \description
prepare_Rd: SequnecAnalysisData-class.Rd:35-37: Dropping empty section \note
prepare_Rd: SequnecAnalysisData-class.Rd:32-34: Dropping empty section \author
prepare_Rd: SequnecAnalysisData-class.Rd:29-31: Dropping empty section \references
prepare_Rd: SequnecAnalysisData-class.Rd:41-44: Dropping empty section \seealso
checkRd: (5) SequnecAnalysisData-class.Rd:0-49: Must have a \description
prepare_Rd: annotate.Rd:7-9: Dropping empty section \description
prepare_Rd: annotate.Rd:39-45: Dropping empty section \value
prepare_Rd: annotate.Rd:52-54: Dropping empty section \note
prepare_Rd: annotate.Rd:49-51: Dropping empty section \author
prepare_Rd: annotate.Rd:46-48: Dropping empty section \references
prepare_Rd: annotate.Rd:58-60: Dropping empty section \seealso
checkRd: (5) annotate.Rd:0-102: Must have a \description
prepare_Rd: diffExp.Rd:33-39: Dropping empty section \value
prepare_Rd: diffExp.Rd:46-48: Dropping empty section \note
prepare_Rd: diffExp.Rd:43-45: Dropping empty section \author
prepare_Rd: diffExp.Rd:40-42: Dropping empty section \references
prepare_Rd: diffExp.Rd:52-54: Dropping empty section \seealso
prepare_Rd: diffExpR.Rd:49-51: Dropping empty section \note
prepare_Rd: diffExpR.Rd:46-48: Dropping empty section \author
prepare_Rd: diffExpR.Rd:43-45: Dropping empty section \references
prepare_Rd: diffExpR.Rd:55-57: Dropping empty section \seealso
prepare_Rd: extract.Rd:7-9: Dropping empty section \description
prepare_Rd: extract.Rd:19-21: Dropping empty section \details
prepare_Rd: extract.Rd:22-28: Dropping empty section \value
prepare_Rd: extract.Rd:35-37: Dropping empty section \note
prepare_Rd: extract.Rd:32-34: Dropping empty section \author
prepare_Rd: extract.Rd:29-31: Dropping empty section \references
prepare_Rd: extract.Rd:41-43: Dropping empty section \seealso
checkRd: (5) extract.Rd:0-66: Must have a \description
prepare_Rd: gcProcess.Rd:24-26: Dropping empty section \details
prepare_Rd: gcProcess.Rd:27-33: Dropping empty section \value
prepare_Rd: gcProcess.Rd:40-42: Dropping empty section \note
prepare_Rd: gcProcess.Rd:37-39: Dropping empty section \author
prepare_Rd: gcProcess.Rd:34-36: Dropping empty section \references
prepare_Rd: gcProcess.Rd:46-48: Dropping empty section \seealso
prepare_Rd: parse.Shimadzu-class.Rd:8-10: Dropping empty section \description
prepare_Rd: parse.Shimadzu-class.Rd:35-37: Dropping empty section \note
prepare_Rd: parse.Shimadzu-class.Rd:32-34: Dropping empty section \author
prepare_Rd: parse.Shimadzu-class.Rd:29-31: Dropping empty section \references
prepare_Rd: parse.Shimadzu-class.Rd:41-44: Dropping empty section \seealso
checkRd: (5) parse.Shimadzu-class.Rd:0-49: Must have a \description
prepare_Rd: parse.shimadzu.Rd:22-28: Dropping empty section \value
prepare_Rd: parse.shimadzu.Rd:35-37: Dropping empty section \note
prepare_Rd: parse.shimadzu.Rd:32-34: Dropping empty section \author
prepare_Rd: parse.shimadzu.Rd:29-31: Dropping empty section \references
prepare_Rd: parse.shimadzu.Rd:41-43: Dropping empty section \seealso
prepare_Rd: plotAllMsSpectra.Rd:19-21: Dropping empty section \details
prepare_Rd: plotAllMsSpectra.Rd:22-28: Dropping empty section \value
prepare_Rd: plotAllMsSpectra.Rd:35-37: Dropping empty section \note
prepare_Rd: plotAllMsSpectra.Rd:32-34: Dropping empty section \author
prepare_Rd: plotAllMsSpectra.Rd:29-31: Dropping empty section \references
prepare_Rd: plotAllMsSpectra.Rd:41-43: Dropping empty section \seealso
prepare_Rd: plotMsSpectrum.Rd:7-9: Dropping empty section \description
prepare_Rd: plotMsSpectrum.Rd:22-24: Dropping empty section \details
prepare_Rd: plotMsSpectrum.Rd:25-31: Dropping empty section \value
prepare_Rd: plotMsSpectrum.Rd:38-40: Dropping empty section \note
prepare_Rd: plotMsSpectrum.Rd:35-37: Dropping empty section \author
prepare_Rd: plotMsSpectrum.Rd:32-34: Dropping empty section \references
prepare_Rd: plotMsSpectrum.Rd:44-46: Dropping empty section \seealso
checkRd: (5) plotMsSpectrum.Rd:0-68: Must have a \description
prepare_Rd: preprocess.Rd:34-36: Dropping empty section \details
prepare_Rd: preprocess.Rd:37-43: Dropping empty section \value
prepare_Rd: preprocess.Rd:50-52: Dropping empty section \note
prepare_Rd: preprocess.Rd:47-49: Dropping empty section \author
prepare_Rd: preprocess.Rd:44-46: Dropping empty section \references
prepare_Rd: preprocess.Rd:56-58: Dropping empty section \seealso
prepare_Rd: rmBaseline.Rd:37-39: Dropping empty section \details
prepare_Rd: rmBaseline.Rd:40-46: Dropping empty section \value
prepare_Rd: rmBaseline.Rd:53-55: Dropping empty section \note
prepare_Rd: rmBaseline.Rd:50-52: Dropping empty section \author
prepare_Rd: rmBaseline.Rd:47-49: Dropping empty section \references
prepare_Rd: rmBaseline.Rd:59-61: Dropping empty section \seealso
prepare_Rd: rnaseqProcess.Rd:51-53: Dropping empty section \note
prepare_Rd: rnaseqProcess.Rd:48-50: Dropping empty section \author
prepare_Rd: rnaseqProcess.Rd:45-47: Dropping empty section \references
prepare_Rd: rnaseqProcess.Rd:57-59: Dropping empty section \seealso
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'show,NcmsProcessData-method':
  ‘NcmsProcessData-class.Rd’ ‘show-methods.Rd’
Rd files with duplicated alias 'show,PreProcessData-method':
  ‘PreProcessData-class.Rd’ ‘show-methods.Rd’
Rd files with duplicated alias 'show,SequnecAnalysisData-method':
  ‘SequnecAnalysisData-class.Rd’ ‘show-methods.Rd’
Rd files with duplicated alias 'show,parse.Shimadzu-method':
  ‘parse.Shimadzu-class.Rd’ ‘show-methods.Rd’
* checking Rd line widths ... NOTE
Rd file 'rmBaseline.Rd':
  \usage lines wider than 90 characters:
     rmBaseline(fldr, bseoffrda = NULL, breaks = 200, qntl = 0, method = "loess", bw = 0.1, SpecNames = list.files(fldr, pattern = "\.*csv\. ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'AverageScan' but not in code:
  lapply

Functions or methods with usage in documentation object 'plotAllMsSpectra' but not in code:
  lapply

Codoc mismatches from documentation object 'rmBaseline':
rmBaseline
  Code: function(fldr, bseoffrda = NULL, breaks = 200, qntl = 0, method
                 = "loess", bw = 0.1, SpecNames = list.files(fldr,
                 pattern = "\\.*csv\\.*"))
  Docs: function(fldr, bseoffrda = NULL, breaks = 200, qntl = 0, method
                 = "loess", bw = 0.1, SpecNames = list.files(fldr,
                 pattern = "\.*csv\.*"))
  Mismatches in argument default values:
    Name: 'SpecNames' Code: list.files(fldr, pattern = "\\.*csv\\.*") Docs: list.files(fldr, pattern = "\.*csv\.*")

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'AverageScan'
  ‘Sample1@MassSpectrum’ ‘AverageScan’
Documented arguments not in \usage in documentation object 'AverageScan':
  ‘x’
Objects in \usage without \alias in documentation object 'AverageScan':
  ‘lapply’

Undocumented arguments in documentation object 'plotAllMsSpectra'
  ‘plotAllMsSpectra’
Objects in \usage without \alias in documentation object 'plotAllMsSpectra':
  ‘lapply’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'::' or ':::' imports not declared from:
  ‘CAMERA’ ‘GOstats’ ‘GenomicRanges’ ‘PROcess’ ‘Rsamtools’ ‘amap’
  ‘limma’ ‘xcms’
'library' or 'require' calls not declared from:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘PROcess’
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... OK

WARNING: There were 6 warnings.
NOTE: There were 5 notes.
See
  ‘/mnt/building/build_2014-06-14-00-12/RF_PKG_CHECK/PKGS/HTDA.Rcheck/00check.log’
for details.

Run time: 28.44 seconds.