Package: clippda

Version: 1.4.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.4.0.tar.gz

StartedAt: 2012-03-23 23:48:58 -0700 (Fri, 23 Mar 2012)

EndedAt: 2012-03-23 23:55:21 -0700 (Fri, 23 Mar 2012)

EllapsedTime: 383.0 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/clippda.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.4.0’
* 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 whether package ‘clippda’ can be installed ... OK
* 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 ... NOTE
Found the following CITATION file(s) in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘clippda’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘clippda.Rnw’ 
** testing if installed package can be loaded

* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.012	0.004	0.016
ZvaluesfrommultinomPlots	1.700	0.016	1.744
aclinicalProteomicsData-class	0.096	0.000	0.100
aclinicalProteomicsData-methods	0.460	0.144	0.603
betweensampleVariance	4.992	0.072	5.201
checkNo.replicates	0.356	0.016	0.401
clippda-package	144.101	0.308	145.909
f	0	0	0
fisherInformation	0.100	0.000	0.097
liverRawData	0.012	0.000	0.014
liver_pheno	0.004	0.000	0.002
liverdata	4.400	0.008	4.446
mostSimilarTwo	0.000	0.000	0.002
negativeIntensitiesCorrection	1.396	0.004	1.445
phenoDataFrame	0.080	0.000	0.095
pheno_urine	0.004	0.000	0.003
preProcRepeatedPeakData	4.049	0.008	4.179
proteomicsExprsData	0.320	0.000	0.336
proteomicspData	0.072	0.004	0.078
replicateCorrelations	7.612	0.004	7.700
sampleClusteredData	1.460	0.000	1.458
sampleSize	91.058	0.152	92.914
sampleSize3DscatterPlots	0.028	0.000	0.026
sampleSizeContourPlots	0.048	0.000	0.050
sampleSizeParameters	44.259	0.044	44.973
sample_technicalVariance	11.216	0.044	11.531
spectrumFilter	3.853	0.004	4.020
ztwo	0	0	0