TCGAbiolinks 2.0.13
Antonio Colaprico , Tiago Chedraoui Silva
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/TCGAbiolinks | | Last Changed Rev: 121923 / Revision: 122332 | | Last Changed Date: 2016-10-05 13:58:10 -0700 (Wed, 05 Oct 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | 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_2.0.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.0.13’
* 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 24.2Mb
sub-directories of 1Mb or more:
data 6.5Mb
doc 16.6Mb
* 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’
checkTumorInput: no visible binding for global variable ‘project’
get.mutation.matrix: no visible binding for global variable ‘Tumor’
update.clinical.with.last.followup: no visible binding for global
variable ‘bcr_patient_barcode’
Undefined global functions or variables:
Tumor bcr_patient_barcode portions project 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GDCquery 70.025 9.213 79.313
GDCdownload 39.187 5.064 110.565
GDCprepare 31.656 3.194 36.293
TCGAanalyze_LevelTab 21.010 1.506 22.530
TCGAanalyze_DEA 9.241 0.380 9.628
TCGAanalyze_DMR 9.083 0.052 9.175
TCGAanalyze_Filtering 8.352 0.253 8.615
TCGAvisualize_oncoprint 6.083 2.014 8.113
TCGAvisualize_starburst 6.427 0.150 6.592
TCGAvisualize_PCA 5.141 0.153 5.303
TCGAanalyze_survival 2.989 2.161 5.154
TCGAvisualize_EAbarplot 5.024 0.109 5.136
GDCprepare_clinic 3.735 1.361 5.102
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.