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 | |
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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_2.2.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.2.10’
* 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 79.3Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 6.4Mb
doc 71.6Mb
* 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 32.389 0.115 44.992
TCGAanalyze_DMR 23.896 0.182 24.249
TCGAanalyze_LevelTab 21.256 1.601 22.878
GDCdownload 14.763 0.732 187.399
GDCprepare 10.562 0.182 19.086
TCGAanalyze_DEA 9.407 0.362 9.781
TCGAanalyze_Filtering 9.137 0.229 9.371
TCGAvisualize_oncoprint 8.509 0.063 12.813
TCGAvisualize_starburst 7.600 0.151 7.767
GDCprepare_clinic 6.805 0.066 11.216
TCGAVisualize_volcano 6.243 0.034 6.289
TCGAanalyze_survival 5.669 0.040 9.531
TCGAanalyze_SurvivalKM 3.786 0.103 11.084
getResults 3.583 0.013 5.339
* 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-3.4-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.