TCGAbiolinks 2.2.10
Antonio Colaprico
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/TCGAbiolinks | | Last Changed Rev: 127636 / Revision: 128728 | | Last Changed Date: 2017-03-22 18:20:19 -0400 (Wed, 22 Mar 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.2.10.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.2.10’
* 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 65.6Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 6.4Mb
doc 57.9Mb
* 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 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’
TCGAvisualize_oncoprint: no visible binding for global variable ‘value’
calculate.pvalues : <anonymous>: no visible binding for global variable
‘aux’
Undefined global functions or variables:
aux portions value
* 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 24.584 0.244 32.856
TCGAanalyze_LevelTab 17.280 0.012 18.169
TCGAanalyze_DMR 16.564 0.008 17.000
GDCdownload 14.372 0.968 151.391
TCGAanalyze_DEA 11.292 0.048 12.453
GDCprepare 9.716 0.240 14.301
TCGAanalyze_Filtering 9.204 0.004 9.638
TCGAvisualize_oncoprint 8.372 0.096 11.217
TCGAvisualize_starburst 5.476 0.000 5.480
GDCprepare_clinic 5.240 0.152 8.182
TCGAanalyze_survival 4.704 0.032 7.083
TCGAanalyze_SurvivalKM 3.420 0.016 9.132
GDCquery_Maf 1.876 0.032 15.753
* 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
‘/home/biocbuild/bbs-3.4-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.