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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### 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
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* 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.
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)