TCGAbiolinks 2.5.7
Antonio Colaprico
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/TCGAbiolinks | | Last Changed Rev: 131796 / Revision: 131943 | | Last Changed Date: 2017-08-07 20:05:58 -0400 (Mon, 07 Aug 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.5.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.5.7’
* 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 ... OK
* checking installed package size ... NOTE
installed size is 80.1Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 6.4Mb
doc 72.4Mb
* 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 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 ... NOTE
GDCquery_clinic: no visible binding for global variable ‘portions’
TCGAanalyze_DEA_Affy: no visible global function definition for
‘limmamakeContrasts’
TCGAanalyze_DEA_Affy: no visible global function definition for
‘limmacontrasts.fit’
TCGAanalyze_analyseGRN: no visible global function definition for
‘knnmi.cross’
TCGAanalyze_networkInference: no visible global function definition for
‘c3net’
TCGAanalyze_networkInference: no visible global function definition for
‘minet’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dNetInduce’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dNetPipeline’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘dCommSignif’
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
‘visNet’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
Undefined global functions or variables:
c3net dCommSignif dNetInduce dNetPipeline knnmi.cross
limmacontrasts.fit limmamakeContrasts minet portions value visNet
* 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 R/sysdata.rda ... 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
GDCquery 28.945 0.084 37.417
TCGAanalyze_DMR 22.244 0.125 23.053
TCGAanalyze_LevelTab 17.464 0.934 18.959
GDCdownload 9.790 0.563 52.146
TCGAanalyze_Filtering 9.584 0.196 10.044
TCGAvisualize_oncoprint 9.117 0.141 11.414
TCGAanalyze_DEA 8.395 0.264 8.786
GDCprepare 8.330 0.171 11.932
TCGAanalyze_survival 7.074 0.088 10.350
GDCprepare_clinic 6.904 0.053 9.353
TCGAvisualize_starburst 6.300 0.134 6.605
TCGAVisualize_volcano 6.234 0.019 6.375
TCGAvisualize_PCA 5.011 0.091 5.246
TCGAanalyze_SurvivalKM 3.183 0.142 11.708
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘DT’
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.