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BioC 3.4: CHECK report for RTCGA on tokay1

This page was generated on 2017-04-15 16:20:19 -0400 (Sat, 15 Apr 2017).

Package 1090/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGA 1.4.0
Marcin Kosinski
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/RTCGA
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCGA
Version: 1.4.0
Command: rm -rf RTCGA.buildbin-libdir RTCGA.Rcheck && mkdir RTCGA.buildbin-libdir RTCGA.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTCGA.buildbin-libdir RTCGA_1.4.0.tar.gz >RTCGA.Rcheck\00install.out 2>&1 && cp RTCGA.Rcheck\00install.out RTCGA-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RTCGA.buildbin-libdir --install="check:RTCGA-install.out" --force-multiarch --no-vignettes --timings RTCGA_1.4.0.tar.gz
StartedAt: 2017-04-15 00:39:51 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:47:51 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 480.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCGA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RTCGA.buildbin-libdir RTCGA.Rcheck && mkdir RTCGA.buildbin-libdir RTCGA.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTCGA.buildbin-libdir RTCGA_1.4.0.tar.gz >RTCGA.Rcheck\00install.out 2>&1 && cp RTCGA.Rcheck\00install.out RTCGA-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RTCGA.buildbin-libdir --install="check:RTCGA-install.out" --force-multiarch --no-vignettes --timings RTCGA_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/RTCGA.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTCGA/DESCRIPTION' ... OK
* this is package 'RTCGA' version '1.4.0'
* 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 whether package 'RTCGA' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ggplot2::%+%' by 'survminer::%+%' when loading 'RTCGA'
See 'C:/Users/biocbuild/bbs-3.4-bioc/meat/RTCGA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
availableDates: no visible binding for global variable '.'
downloadTCGA: no visible binding for global variable '.'
ggbiplot: no visible binding for global variable 'xvar'
ggbiplot: no visible binding for global variable 'yvar'
ggbiplot: no visible global function definition for 'muted'
ggbiplot: no visible binding for global variable 'varname'
ggbiplot: no visible binding for global variable 'angle'
ggbiplot: no visible binding for global variable 'hjust'
read.mutations: no visible binding for global variable '.'
read.rnaseq: no visible binding for global variable '.'
survivalTCGA: no visible binding for global variable 'times'
whichDateToUse: no visible binding for global variable '.'
Undefined global functions or variables:
  . angle hjust muted times varname xvar yvar
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
expressionsTCGA 49.92   3.94   56.57
boxplotTCGA     35.25   3.31   41.52
heatmapTCGA     25.31   3.01   28.32
kmTCGA          11.48   0.02   12.85
survivalTCGA    10.29   0.04   10.35
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
expressionsTCGA 67.55   0.90   68.50
boxplotTCGA     45.86   1.49   47.34
heatmapTCGA     34.42   0.04   34.47
kmTCGA          14.16   0.02   14.18
survivalTCGA    12.56   0.00   12.56
mutationsTCGA    5.97   0.00    5.97
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/RTCGA.Rcheck/00check.log'
for details.


RTCGA.Rcheck/00install.out:


install for i386

* installing *source* package 'RTCGA' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::%+%' by 'survminer::%+%' when loading 'RTCGA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::%+%' by 'survminer::%+%' when loading 'RTCGA'

install for x64

* installing *source* package 'RTCGA' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::%+%' by 'survminer::%+%' when loading 'RTCGA'
* MD5 sums
packaged installation of 'RTCGA' as RTCGA_1.4.0.zip
* DONE (RTCGA)

RTCGA.Rcheck/examples_i386/RTCGA-Ex.timings:

nameusersystemelapsed
RTCGA-package000
boxplotTCGA35.25 3.3141.52
checkTCGA0.610.062.11
convertTCGA1.660.191.84
datasetsTCGA0.010.000.02
downloadTCGA0.050.000.57
expressionsTCGA49.92 3.9456.57
heatmapTCGA25.31 3.0128.32
infoTCGA0.880.000.97
installTCGA000
kmTCGA11.48 0.0212.85
mutationsTCGA4.640.004.64
pcaTCGA000
readTCGA000
survivalTCGA10.29 0.0410.35
theme_RTCGA3.800.003.79

RTCGA.Rcheck/examples_x64/RTCGA-Ex.timings:

nameusersystemelapsed
RTCGA-package000
boxplotTCGA45.86 1.4947.34
checkTCGA0.840.062.23
convertTCGA3.070.503.58
datasetsTCGA000
downloadTCGA0.030.020.32
expressionsTCGA67.55 0.9068.50
heatmapTCGA34.42 0.0434.47
infoTCGA1.090.001.19
installTCGA000
kmTCGA14.16 0.0214.18
mutationsTCGA5.970.005.97
pcaTCGA000
readTCGA000
survivalTCGA12.56 0.0012.56
theme_RTCGA4.940.004.94