TCGAbiolinks 2.3.23
Antonio Colaprico
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TCGAbiolinks | | Last Changed Rev: 128969 / Revision: 129046 | | Last Changed Date: 2017-04-20 13:57:30 -0400 (Thu, 20 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | 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_2.3.23.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘2.3.23’
* 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 81.1Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 6.4Mb
doc 73.3Mb
* 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 ... NOTE
Namespaces in Imports field not imported from:
‘gplots’ ‘xtable’
All declared Imports should be used.
* 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 33.553 0.131 47.878
TCGAanalyze_DMR 26.377 0.152 28.973
TCGAanalyze_LevelTab 19.136 1.305 20.686
GDCdownload 17.693 0.864 97.196
TCGAvisualize_oncoprint 10.076 0.098 13.599
TCGAanalyze_Filtering 9.865 0.286 10.208
GDCprepare 9.423 0.173 15.761
TCGAanalyze_DEA 9.183 0.321 10.789
TCGAVisualize_volcano 8.061 0.033 9.182
GDCprepare_clinic 7.557 0.068 11.371
TCGAanalyze_survival 7.415 0.033 10.211
TCGAvisualize_starburst 7.189 0.187 7.442
TCGAvisualize_PCA 5.365 0.135 5.539
TCGAanalyze_SurvivalKM 3.347 0.090 9.661
matchedMetExp 3.182 0.018 5.173
GDCquery_clinic 0.948 0.018 7.753
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.