TCGAbiolinks 2.2.10
Antonio Colaprico
| 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/TCGAbiolinks | | Last Changed Rev: 127636 / Revision: 128728 | | Last Changed Date: 2017-03-22 18:20:19 -0400 (Wed, 22 Mar 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ TIMEOUT ] | OK | |
| morelia | 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 TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && mkdir TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.2.10.tar.gz >TCGAbiolinks.Rcheck\00install.out 2>&1 && cp TCGAbiolinks.Rcheck\00install.out TCGAbiolinks-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=TCGAbiolinks.buildbin-libdir --install="check:TCGAbiolinks-install.out" --force-multiarch --no-vignettes --timings TCGAbiolinks_2.2.10.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/TCGAbiolinks.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 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.2.10'
* 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 'TCGAbiolinks' can be installed ... OK
* checking installed package size ... NOTE
installed size is 64.9Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 6.4Mb
doc 57.2Mb
* 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
* 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
GDCquery_clinic: no visible binding for global variable 'portions'
TCGAvisualize_oncoprint: no visible binding for global variable 'value'
calculate.pvalues : <anonymous>: no visible binding for global variable
'aux'
Undefined global functions or variables:
aux portions 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GDCquery 16.81 0.08 24.28
TCGAanalyze_LevelTab 16.71 0.05 16.75
TCGAanalyze_DMR 13.97 0.10 14.07
GDCdownload 10.17 0.75 723.88
TCGAanalyze_DEA 9.92 0.06 9.98
TCGAanalyze_Filtering 7.89 0.00 7.89
GDCprepare 6.39 0.12 11.54
TCGAvisualize_starburst 5.63 0.05 5.67
TCGAvisualize_oncoprint 5.31 0.03 18.99
TCGAanalyze_survival 4.16 0.05 6.78
GDCprepare_clinic 3.20 0.03 9.40
TCGAanalyze_SurvivalKM 2.71 0.01 8.76
GDCquery_Maf 1.43 0.05 23.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GDCquery 17.46 0.03 24.82
TCGAanalyze_LevelTab 15.60 0.02 15.61
TCGAanalyze_DMR 15.41 0.05 15.45
GDCdownload 8.86 0.57 722.76
TCGAanalyze_DEA 8.77 0.04 8.81
TCGAanalyze_Filtering 7.79 0.00 7.80
GDCprepare 7.12 0.24 38.05
TCGAvisualize_oncoprint 6.13 0.07 9.25
TCGAvisualize_starburst 5.50 0.01 5.52
TCGAanalyze_survival 5.28 0.00 7.53
GDCprepare_clinic 3.32 0.00 6.37
TCGAanalyze_SurvivalKM 2.41 0.03 8.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
install for i386
* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'TCGAbiolinks' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAbiolinks' as TCGAbiolinks_2.2.10.zip
* DONE (TCGAbiolinks)