BioC 3.2: CHECK report for TCGAbiolinks on perceval

Package: TCGAbiolinks

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_1.0.1.tar.gz

StartedAt: 2015-10-27 12:50:33 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 13:00:25 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 591.3 seconds

RetCode: 0

Status:  OK

CheckDir: TCGAbiolinks.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.0.1’
* 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/52s] OK
* checking installed package size ... NOTE
  installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
    doc    8.0Mb
    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 ... [107s/123s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
TCGAanalyze_LevelTab      26.190  0.742  26.955
TCGAanalyze_DEA           12.339  0.378  12.700
TCGAanalyze_Filtering     10.094  0.323  10.411
TCGAvisualize_PCA          5.615  0.188   5.800
TCGAanalyze_Normalization  5.145  0.165   5.306
TCGAanalyze_EAcomplete     4.985  0.092   5.075
TCGAquery                  3.851  0.048   8.096
TCGAquery_Version          3.276  0.068   8.934
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [24s/40s]
 [25s/41s] 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 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
TCGAVisualize_volcano	0.366	0.017	0.382
TCGAanalyze_DEA	12.339	0.378	12.700
TCGAanalyze_DEA_Affy	0.000	0.000	0.001
TCGAanalyze_DMR	4.576	0.095	4.772
TCGAanalyze_EA	0.001	0.000	0.001
TCGAanalyze_EAcomplete	4.985	0.092	5.075
TCGAanalyze_Filtering	10.094	0.323	10.411
TCGAanalyze_LevelTab	26.190	0.742	26.955
TCGAanalyze_Normalization	5.145	0.165	5.306
TCGAanalyze_Preprocessing	0.136	0.022	0.156
TCGAanalyze_SurvivalKM	0.018	0.000	0.017
TCGAanalyze_survival	0.379	0.005	0.384
TCGAdownload	1.252	0.076	4.900
TCGAprepare	0.627	0.065	2.110
TCGAprepare_Affy	0.000	0.001	0.000
TCGAprepare_elmer	0.009	0.002	0.012
TCGAquery	3.851	0.048	8.096
TCGAquery_Investigate	0.019	0.001	0.020
TCGAquery_MatchedCoupledSampleTypes	0.001	0.000	0.001
TCGAquery_SampleTypes	0.002	0.001	0.001
TCGAquery_Social	0.245	0.013	0.926
TCGAquery_Version	3.276	0.068	8.934
TCGAquery_clinic	0.134	0.009	1.390
TCGAquery_clinicFilt	0.051	0.004	0.055
TCGAquery_integrate	0.124	0.002	0.126
TCGAquery_maf	0.001	0.000	0.000
TCGAquery_samplesfilter	0.061	0.000	0.062
TCGAquery_subtype	0.002	0.000	0.002
TCGAvisualize_BarPlot	0.019	0.001	0.019
TCGAvisualize_EAbarplot	4.427	0.226	4.650
TCGAvisualize_Heatmap	0.018	0.000	0.018
TCGAvisualize_PCA	5.615	0.188	5.800
TCGAvisualize_Tables	0.066	0.001	0.066
TCGAvisualize_meanMethylation	0.393	0.005	0.398
TCGAvisualize_starburst	1.999	0.117	2.121
calculate.pvalues	0.001	0.000	0.001
diffmean	0.001	0.000	0.001