BioC 3.2: CHECK report for TCGAbiolinks on perceval

Package: TCGAbiolinks

Version: 0.99.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_0.99.1.tar.gz

StartedAt: 2015-08-13 07:20:32 -0700 (Thu, 13 Aug 2015)

EndedAt: 2015-08-13 07:36:03 -0700 (Thu, 13 Aug 2015)

EllapsedTime: 931.3 seconds

RetCode: 0

Status:  OK

CheckDir: TCGAbiolinks.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_0.99.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.2.2 RC (2015-08-07 r68909)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAbiolinks/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TCGAbiolinks’ version ‘0.99.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘TCGAbiolinks’ can be installed ... [51s/69s] OK
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
    doc    1.5Mb
    R      1.7Mb
* 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 ... 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 ... 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 ... NOTE
  Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [90s/133s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
TCGAanalyze_LevelTab      18.554  1.768  21.651
TCGAanalyze_DEA           12.542  0.534  21.503
TCGAvisualize_PCA          6.214  0.270   7.822
TCGAanalyze_DMR            5.740  0.196  11.830
TCGAanalyze_Filtering      5.415  0.239   5.784
TCGAanalyze_Normalization  5.074  0.206   5.458
TCGAvisualize_EAbarplot    4.872  0.321   6.051
TCGAdownload               1.320  0.084   9.900
TCGAprepare                0.502  0.090   5.829
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.

* installing *source* package ‘TCGAbiolinks’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCGAbiolinks)

name	user	system	elapsed
TCGAanalyze_DEA	12.542	0.534	21.503
TCGAanalyze_DMR	5.740	0.196	11.830
TCGAanalyze_EA	0.001	0.000	0.001
TCGAanalyze_EAcomplete	4.324	0.274	4.688
TCGAanalyze_Filtering	5.415	0.239	5.784
TCGAanalyze_LevelTab	18.554	1.768	21.651
TCGAanalyze_Normalization	5.074	0.206	5.458
TCGAanalyze_SurvivalKM	0.001	0.001	0.030
TCGAanalyze_survival	0.378	0.006	0.533
TCGAdownload	1.320	0.084	9.900
TCGAintegrate	0.111	0.001	0.112
TCGAinvestigate	0.001	0.001	0.001
TCGAprepare	0.502	0.090	5.829
TCGAquery	0.092	0.001	0.093
TCGAquery_MatchedCoupledSampleTypes	0.001	0.000	0.001
TCGAquery_SampleTypes	0.001	0.000	0.002
TCGAquery_Version	0.168	0.007	1.891
TCGAquery_clinic	0.124	0.007	1.562
TCGAquery_clinicFilt	0.041	0.005	0.046
TCGAquery_samplesfilter	0.065	0.001	0.066
TCGAquery_subtypes	0.000	0.001	0.085
TCGAsocial	0.269	0.019	1.495
TCGAvisualize_EAbarplot	4.872	0.321	6.051
TCGAvisualize_PCA	6.214	0.270	7.822
TCGAvisualize_meanMethylation	0.384	0.008	1.003
TCGAvisualize_starburst	2.082	0.138	2.229
calculate.pvalues	0.001	0.000	0.001
diffmean	0.001	0.000	0.001