R Development Page

WaveSeqR log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2013-11-26-00-08/RF_PKG_CHECK/PKGS/WaveSeqR.Rcheck'
* using R version 3.0.2 Patched (2013-11-22 r64286)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'WaveSeqR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'WaveSeqR' version '1.0.3'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Apratim Mitra , Jiuzhou Song
'
New submission
* 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 whether package 'WaveSeqR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
[1] "waveSeqR.Rnw"
See the information on INDEX files and package subdirectories in the
chapter 'Creating R packages' of the 'Writing R Extensions' manual.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: WaveSeqR-package.Rd:35-37: Dropping empty section \references
prepare_Rd: checkFolderHierarchy.Rd:21-23: Dropping empty section \examples
prepare_Rd: compareWithControl.Rd:57-59: Dropping empty section \note
prepare_Rd: compareWithControl.Rd:51-53: Dropping empty section \references
prepare_Rd: compareWithControl.Rd:68-70: Dropping empty section \examples
prepare_Rd: controlFDR.Rd:70-72: Dropping empty section \note
prepare_Rd: controlFDR.Rd:64-66: Dropping empty section \references
prepare_Rd: controlFDR.Rd:80-82: Dropping empty section \examples
prepare_Rd: gabp_peaks.Rd:28-30: Dropping empty section \details
prepare_Rd: gapDiagnostic.Rd:33-35: Dropping empty section \details
prepare_Rd: gapDiagnostic.Rd:46-48: Dropping empty section \note
prepare_Rd: gapDiagnostic.Rd:40-42: Dropping empty section \references
prepare_Rd: gapPeaks.Rd:30-32: Dropping empty section \details
prepare_Rd: gapPeaks.Rd:48-50: Dropping empty section \note
prepare_Rd: gapPeaks.Rd:42-44: Dropping empty section \references
prepare_Rd: gapPeaks.Rd:54-56: Dropping empty section \seealso
prepare_Rd: getConfidenceInterval.Rd:27-29: Dropping empty section \details
prepare_Rd: getConfidenceInterval.Rd:30-36: Dropping empty section \value
prepare_Rd: getConfidenceInterval.Rd:43-45: Dropping empty section \note
prepare_Rd: getConfidenceInterval.Rd:37-39: Dropping empty section \references
prepare_Rd: getConfidenceInterval.Rd:49-51: Dropping empty section \seealso
prepare_Rd: getConfidenceInterval.Rd:52-53: Dropping empty section \examples
prepare_Rd: getPeakReads.Rd:26-28: Dropping empty section \details
prepare_Rd: getPeakReads.Rd:39-41: Dropping empty section \note
prepare_Rd: getPeakReads.Rd:33-35: Dropping empty section \references
prepare_Rd: getPeakReads.Rd:47-49: Dropping empty section \seealso
prepare_Rd: getPeakReads.Rd:50-53: Dropping empty section \examples
prepare_Rd: getPeakReads_batch.Rd:29-31: Dropping empty section \details
prepare_Rd: getPeakReads_batch.Rd:32-34: Dropping empty section \value
prepare_Rd: getPeakReads_batch.Rd:41-43: Dropping empty section \note
prepare_Rd: getPeakReads_batch.Rd:35-37: Dropping empty section \references
prepare_Rd: getPeakReads_batch.Rd:52-55: Dropping empty section \examples
prepare_Rd: getThresholdDistribution.Rd:50-56: Dropping empty section \value
prepare_Rd: getThresholdDistribution.Rd:57-59: Dropping empty section \references
prepare_Rd: getThresholdDistribution.Rd:76-78: Dropping empty section \examples
prepare_Rd: noControlFDR.Rd:60-62: Dropping empty section \note
prepare_Rd: noControlFDR.Rd:54-56: Dropping empty section \references
prepare_Rd: noControlFDR.Rd:69-71: Dropping empty section \examples
prepare_Rd: preprocess.Rd:37-39: Dropping empty section \details
prepare_Rd: preprocess.Rd:40-46: Dropping empty section \value
prepare_Rd: preprocess.Rd:47-49: Dropping empty section \references
prepare_Rd: preprocess.Rd:60-62: Dropping empty section \seealso
prepare_Rd: preprocess.Rd:63-65: Dropping empty section \examples
prepare_Rd: randomizedBackground.Rd:50-52: Dropping empty section \note
prepare_Rd: randomizedBackground.Rd:44-46: Dropping empty section \references
prepare_Rd: randomizedBackground.Rd:62-64: Dropping empty section \examples
prepare_Rd: waveletThresholding.Rd:61-67: Dropping empty section \value
prepare_Rd: waveletThresholding.Rd:68-70: Dropping empty section \references
prepare_Rd: waveletThresholding.Rd:84-86: Dropping empty section \examples
prepare_Rd: waveseq.Rd:137-139: Dropping empty section \note
prepare_Rd: waveseq.Rd:131-133: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'R:/run/building/build_2013-11-26-00-08/RF_PKG_CHECK/PKGS/WaveSeqR.Rcheck/00_pkg_src/WaveSeqR/man/compareWithControl.Rd':
  \usage lines wider than 90 characters:
     compareWithControl(peaks, chip, control, winsize = 200, minreads = 8, binom.sided = "two.sided")

Rd file 'R:/run/building/build_2013-11-26-00-08/RF_PKG_CHECK/PKGS/WaveSeqR.Rcheck/00_pkg_src/WaveSeqR/man/getThresholdDistribution.Rd':
  \usage lines wider than 90 characters:
     getThresholdDistribution(infile, outdir, exptname, mother = "morlet", N = 5000, maxscale = 12, p.min = 0.001, p.max = 0.3)

Rd file 'R:/run/building/build_2013-11-26-00-08/RF_PKG_CHECK/PKGS/WaveSeqR.Rcheck/00_pkg_src/WaveSeqR/man/waveletThresholding.Rd':
  \usage lines wider than 90 characters:
     waveletThresholding(infile, outdir, exptname, mother = "morlet", winsize = 200, minsig = 2, minsigscale = 3, 

Rd file 'R:/run/building/build_2013-11-26-00-08/RF_PKG_CHECK/PKGS/WaveSeqR.Rcheck/00_pkg_src/WaveSeqR/man/waveseq.Rd':
  \usage lines wider than 90 characters:
     waveseq(chip, control=NA, outdir, exptname, preprocess = TRUE, redundancy = TRUE, thresdist = TRUE, 
             peak.calling = TRUE, mother = "morlet", winsize = 200, fragsize = 150, gap = 0, minreads = 8,
             samplesize = 1e6, adj.method = "fdr", p.thres = 0.2, maxscale = 12, N = 5000, minsig = 2, 
             minsigscale = 3, maxsigscale = -1, p.min = 0.001, p.max = 0.3, binom.sided = "two.sided")

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
Data codoc mismatches from documentation object 'gabp_peaks':
Variables in data frame 'gabp_peaks'
  Code: V1 V2 V3 V4 V5 V6 V7 V8
  Docs: adj.p.value chip_reads chr control_reads end fold_change
        p.value start

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
WaveSeqR-package 15.53   0.83   16.44
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
   'waveSeqR.Rnw' ... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  'R:/run/building/build_2013-11-26-00-08/RF_PKG_CHECK/PKGS/WaveSeqR.Rcheck/00check.log'
for details.

Run time: 72 seconds.