BioC 3.2: CHECK report for TCGAbiolinks on linux1.bioconductor.org

Package: TCGAbiolinks

Version: 1.0.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_1.0.1.tar.gz

StartedAt: 2015-10-27 08:41:26 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:48:33 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 426.6 seconds

RetCode: 0

Status:  OK

CheckDir: TCGAbiolinks.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [40s/41s] OK
* checking installed package size ... NOTE
  installed size is 15.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   6.2Mb
    doc    6.9Mb
* 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 ... [88s/94s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
TCGAanalyze_LevelTab      21.538  0.087  21.638
TCGAanalyze_DEA           12.232  0.052  12.276
TCGAanalyze_Filtering      9.033  0.000   9.041
TCGAvisualize_PCA          5.428  0.004   5.441
TCGAanalyze_Normalization  5.191  0.001   5.190
TCGAquery                  3.096  0.012   5.006
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [18s/24s]
 [18s/24s] 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
  ‘/home/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	0.324	0.004	0.328
TCGAanalyze_DEA	12.232	0.052	12.276
TCGAanalyze_DEA_Affy	0.001	0.000	0.000
TCGAanalyze_DMR	3.993	0.020	4.017
TCGAanalyze_EA	0.001	0.000	0.001
TCGAanalyze_EAcomplete	3.787	0.004	3.798
TCGAanalyze_Filtering	9.033	0.000	9.041
TCGAanalyze_LevelTab	21.538	0.087	21.638
TCGAanalyze_Normalization	5.191	0.001	5.190
TCGAanalyze_Preprocessing	0.139	0.000	0.140
TCGAanalyze_SurvivalKM	0.021	0.000	0.021
TCGAanalyze_survival	0.290	0.000	0.289
TCGAdownload	0.736	0.000	1.712
TCGAprepare	0.378	0.000	0.781
TCGAprepare_Affy	0.001	0.000	0.000
TCGAprepare_elmer	0.005	0.000	0.004
TCGAquery	3.096	0.012	5.006
TCGAquery_Investigate	0.022	0.000	0.023
TCGAquery_MatchedCoupledSampleTypes	0.001	0.000	0.002
TCGAquery_SampleTypes	0.002	0.000	0.001
TCGAquery_Social	0.175	0.000	0.241
TCGAquery_Version	1.818	0.004	3.992
TCGAquery_clinic	0.059	0.004	0.408
TCGAquery_clinicFilt	0.034	0.000	0.034
TCGAquery_integrate	0.099	0.000	0.099
TCGAquery_maf	0	0	0
TCGAquery_samplesfilter	0.056	0.000	0.056
TCGAquery_subtype	0.002	0.000	0.002
TCGAvisualize_BarPlot	0.022	0.000	0.022
TCGAvisualize_EAbarplot	4.347	0.004	4.351
TCGAvisualize_Heatmap	0.021	0.000	0.021
TCGAvisualize_PCA	5.428	0.004	5.441
TCGAvisualize_Tables	0.039	0.000	0.040
TCGAvisualize_meanMethylation	0.427	0.000	0.426
TCGAvisualize_starburst	1.815	0.004	1.818
calculate.pvalues	0.001	0.000	0.001
diffmean	0.001	0.000	0.001