TCGAbiolinks 1.1.4
Antonio Colaprico , Tiago Chedraoui Silva
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TCGAbiolinks | | Last Changed Rev: 109913 / Revision: 109948 | | Last Changed Date: 2015-10-25 18:12:58 -0400 (Sun, 25 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TCGAbiolinks_1.1.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/TCGAbiolinks.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.1.4’
* 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 ... [45s/49s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘reshape2::dcast’ when loading ‘TCGAbiolinks’
See ‘/home/biocbuild/bbs-3.3-bioc/meat/TCGAbiolinks.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 18.2Mb
sub-directories of 1Mb or more:
R 1.7Mb
data 6.2Mb
doc 10.0Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘sjPlot:::sj.setGeomColors’ ‘sjmisc:::autoSetValueLabels’
‘sjmisc:::autoSetVariableLabels’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TCGAanalyze_copynumber: no visible binding for global variable
‘geneInfo’
Undefined global functions or variables:
geneInfo
* 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 ... [86s/93s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAanalyze_LevelTab 21.656 0.136 21.785
TCGAanalyze_Filtering 10.155 0.000 10.165
TCGAanalyze_DEA 10.112 0.036 10.148
TCGAquery_Version 3.198 0.012 5.799
TCGAquery 3.141 0.024 5.310
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [20s/26s]
[20s/26s] 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: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/TCGAbiolinks.Rcheck/00check.log’
for details.
* installing *source* package ‘TCGAbiolinks’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘reshape2::dcast’ when loading ‘TCGAbiolinks’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘reshape2::dcast’ when loading ‘TCGAbiolinks’
* DONE (TCGAbiolinks)