TCGAbiolinks 2.5.9
Antonio Colaprico
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/TCGAbiolinks | | Branch: RELEASE_3_5 | | Last Commit: 3cac966 | | Last Changed Date: 2017-09-14 20:23:09 -0400 (Thu, 14 Sep 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.5.9.tar.gz >TCGAbiolinks.Rcheck\00install.out 2>&1 && cp TCGAbiolinks.Rcheck\00install.out TCGAbiolinks-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=TCGAbiolinks.buildbin-libdir --install="check:TCGAbiolinks-install.out" --force-multiarch --no-vignettes --timings TCGAbiolinks_2.5.9.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/TCGAbiolinks.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '2.5.9'
* 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 60.6Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 2.3Mb
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'
getTSS: no visible global function definition for 'promoters'
Undefined global functions or variables:
c3net dCommSignif dNetInduce dNetPipeline knnmi.cross
limmacontrasts.fit limmamakeContrasts minet portions promoters 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
TCGAvisualize_starburst 84.28 2.50 128.11
TCGAanalyze_LevelTab 22.89 0.05 23.24
GDCquery 20.97 0.11 28.46
TCGAanalyze_DMR 16.41 0.06 16.47
TCGAanalyze_DEA 9.53 0.22 9.75
TCGAanalyze_Filtering 8.66 0.00 8.65
GDCdownload 7.17 1.25 80.59
TCGAanalyze_survival 7.76 0.03 13.00
GDCprepare 6.61 0.16 10.42
TCGAanalyze_Normalization 5.26 0.00 5.28
TCGAVisualize_volcano 5.12 0.00 5.12
GDCprepare_clinic 4.99 0.05 8.16
TCGAanalyze_SurvivalKM 2.66 0.01 21.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
TCGAvisualize_starburst 83.94 2.51 122.14
TCGAanalyze_LevelTab 23.47 0.06 23.54
TCGAanalyze_DMR 20.38 0.11 20.49
GDCquery 18.33 0.08 25.13
TCGAanalyze_Filtering 14.75 0.02 14.76
TCGAanalyze_DEA 10.36 0.10 10.46
GDCdownload 8.09 1.08 75.94
GDCprepare 7.69 0.16 11.54
TCGAVisualize_volcano 7.29 0.01 7.29
TCGAanalyze_survival 7.16 0.02 12.62
TCGAvisualize_PCA 6.40 0.00 6.41
TCGAanalyze_Normalization 5.79 0.00 5.80
GDCprepare_clinic 5.18 0.03 8.39
TCGAanalyze_EAcomplete 5.18 0.01 5.20
TCGAanalyze_SurvivalKM 2.11 0.06 20.28
* 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-3.5-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_2.5.9.zip
* DONE (TCGAbiolinks)