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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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_2.0.13.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/TCGAbiolinks.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.0.13’
* 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 20.8Mb
sub-directories of 1Mb or more:
data 6.5Mb
doc 13.2Mb
* 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 38.875 3.994 43.184
GDCdownload 22.480 3.123 107.744
GDCprepare 19.000 1.480 21.850
TCGAanalyze_LevelTab 19.504 0.023 19.582
TCGAanalyze_DEA 10.797 0.026 10.899
TCGAanalyze_Filtering 8.123 0.001 8.144
TCGAanalyze_DMR 7.229 0.008 7.293
TCGAvisualize_oncoprint 6.145 0.941 7.122
TCGAvisualize_starburst 5.408 0.019 5.487
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.