RTCGA 1.2.5
Marcin Kosinski
| 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/RTCGA | | Last Changed Rev: 121552 / Revision: 122332 | | Last Changed Date: 2016-09-29 07:13:14 -0700 (Thu, 29 Sep 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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### rm -rf RTCGA.buildbin-libdir RTCGA.Rcheck && mkdir RTCGA.buildbin-libdir RTCGA.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTCGA.buildbin-libdir RTCGA_1.2.5.tar.gz >RTCGA.Rcheck\00install.out 2>&1 && cp RTCGA.Rcheck\00install.out RTCGA-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RTCGA.buildbin-libdir --install="check:RTCGA-install.out" --force-multiarch --no-vignettes --timings RTCGA_1.2.5.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/RTCGA.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.2.5'
* 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 ... OK
* 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 70.36 0.61 81.39
boxplotTCGA 48.11 0.92 56.81
heatmapTCGA 35.27 0.11 35.78
kmTCGA 15.07 0.03 15.41
survivalTCGA 10.72 0.00 10.72
theme_RTCGA 5.56 0.00 5.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
expressionsTCGA 86.67 0.39 95.39
boxplotTCGA 59.17 0.90 61.53
heatmapTCGA 51.56 0.07 52.36
kmTCGA 16.29 0.02 16.30
survivalTCGA 14.68 0.00 14.68
mutationsTCGA 6.25 0.00 6.25
theme_RTCGA 6.13 0.00 6.14
checkTCGA 0.58 0.20 6.35
* 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 NOTE
See
'E:/biocbld/bbs-3.3-bioc/meat/RTCGA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'RTCGA' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'RTCGA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGA' as RTCGA_1.2.5.zip
* DONE (RTCGA)