TCGAbiolinks 2.5.7
Antonio Colaprico
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TCGAbiolinks | | Last Changed Rev: 131795 / Revision: 131943 | | Last Changed Date: 2017-08-07 20:03:07 -0400 (Mon, 07 Aug 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / 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-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.5.7.tar.gz >TCGAbiolinks.Rcheck\00install.out 2>&1 && cp TCGAbiolinks.Rcheck\00install.out TCGAbiolinks-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TCGAbiolinks.buildbin-libdir --install="check:TCGAbiolinks-install.out" --force-multiarch --no-vignettes --timings TCGAbiolinks_2.5.7.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '2.5.7'
* 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 64.7Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 6.4Mb
doc 57.0Mb
* 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
* 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'
TCGAanalyze_DEA_Affy: no visible global function definition for
'limmamakeContrasts'
TCGAanalyze_DEA_Affy: no visible global function definition for
'limmacontrasts.fit'
TCGAanalyze_analyseGRN: no visible global function definition for
'knnmi.cross'
TCGAanalyze_networkInference: no visible global function definition for
'c3net'
TCGAanalyze_networkInference: no visible global function definition for
'minet'
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
'dNetInduce'
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
'dNetPipeline'
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
'dCommSignif'
TCGAvisualize_SurvivalCoxNET: no visible global function definition for
'visNet'
TCGAvisualize_oncoprint: no visible binding for global variable 'value'
Undefined global functions or variables:
c3net dCommSignif dNetInduce dNetPipeline knnmi.cross
limmacontrasts.fit limmamakeContrasts minet portions value visNet
* 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
TCGAanalyze_DMR 24.94 0.23 25.64
TCGAanalyze_LevelTab 24.00 0.10 24.36
GDCquery 19.04 0.04 26.50
TCGAanalyze_Filtering 13.16 0.01 13.18
TCGAanalyze_DEA 12.46 0.16 12.62
GDCdownload 9.14 1.06 81.81
TCGAanalyze_survival 9.03 0.03 11.92
TCGAvisualize_starburst 7.11 0.00 7.11
GDCprepare 6.84 0.23 10.44
TCGAvisualize_PCA 6.66 0.00 6.65
TCGAanalyze_Normalization 5.98 0.04 6.06
GDCprepare_clinic 5.59 0.07 8.60
TCGAanalyze_EAcomplete 5.42 0.02 5.43
TCGAVisualize_volcano 5.32 0.00 5.32
TCGAanalyze_SurvivalKM 3.39 0.02 11.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAanalyze_DMR 21.15 0.02 21.17
GDCquery 20.39 0.07 27.89
TCGAanalyze_LevelTab 16.63 0.01 16.66
TCGAanalyze_Filtering 11.62 0.00 11.62
TCGAanalyze_DEA 11.58 0.01 11.59
GDCprepare 10.64 0.14 14.22
GDCdownload 7.57 0.81 61.05
TCGAanalyze_survival 7.92 0.05 10.81
TCGAvisualize_starburst 6.85 0.03 6.87
GDCprepare_clinic 6.80 0.06 10.43
TCGAanalyze_Normalization 6.57 0.00 6.58
TCGAvisualize_PCA 6.09 0.00 6.09
TCGAVisualize_volcano 5.93 0.00 5.94
TCGAanalyze_SurvivalKM 2.68 0.08 10.64
* 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 ... NOTE
'library' or 'require' call not declared from: 'DT'
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/TCGAbiolinks.Rcheck/00check.log'
for details.
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_2.5.7.zip
* DONE (TCGAbiolinks)