TCGAbiolinks 2.0.13
Antonio Colaprico , Tiago Chedraoui Silva
| 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/TCGAbiolinks | | Last Changed Rev: 121923 / Revision: 122332 | | Last Changed Date: 2016-10-05 13:58:10 -0700 (Wed, 05 Oct 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 TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && mkdir TCGAbiolinks.buildbin-libdir TCGAbiolinks.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TCGAbiolinks.buildbin-libdir TCGAbiolinks_2.0.13.tar.gz >TCGAbiolinks.Rcheck\00install.out 2>&1 && cp TCGAbiolinks.Rcheck\00install.out TCGAbiolinks-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=TCGAbiolinks.buildbin-libdir --install="check:TCGAbiolinks-install.out" --force-multiarch --no-vignettes --timings TCGAbiolinks_2.0.13.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/TCGAbiolinks.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 'TCGAbiolinks/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TCGAbiolinks' version '2.0.13'
* 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 18.7Mb
sub-directories of 1Mb or more:
data 6.5Mb
doc 11.1Mb
* 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'
checkTumorInput: no visible binding for global variable 'project'
get.mutation.matrix: no visible binding for global variable 'Tumor'
update.clinical.with.last.followup: no visible binding for global
variable 'bcr_patient_barcode'
Undefined global functions or variables:
Tumor bcr_patient_barcode portions project 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 ... NOTE
Note: found 1 marked UTF-8 string
* 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 66.07 11.56 77.80
GDCdownload 35.80 6.52 97.66
GDCprepare 29.73 4.21 35.46
TCGAanalyze_LevelTab 26.54 0.01 26.57
TCGAanalyze_DEA 15.54 0.00 15.54
TCGAanalyze_Filtering 12.54 0.00 12.54
TCGAvisualize_oncoprint 7.50 2.46 10.10
TCGAvisualize_starburst 9.85 0.02 9.85
TCGAanalyze_DMR 9.69 0.05 9.73
TCGAanalyze_Normalization 6.66 0.00 6.66
TCGAvisualize_PCA 6.60 0.02 6.61
GDCquery_clinic 3.31 2.73 6.09
TCGAanalyze_survival 3.43 2.20 5.63
GDCprepare_clinic 3.95 1.58 5.60
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GDCquery 63.50 11.30 78.82
GDCdownload 41.20 7.01 134.50
GDCprepare 30.65 3.83 37.46
TCGAanalyze_LevelTab 27.32 0.00 28.26
TCGAanalyze_DEA 16.01 0.00 16.00
TCGAanalyze_Filtering 15.32 0.01 15.66
TCGAanalyze_DMR 12.04 0.06 12.41
TCGAvisualize_oncoprint 8.91 2.60 12.71
TCGAvisualize_starburst 11.31 0.00 11.31
TCGAvisualize_PCA 8.11 0.00 8.11
TCGAvisualize_meanMethylation 6.66 0.02 6.71
TCGAanalyze_Normalization 6.61 0.00 6.81
GDCquery_clinic 3.71 2.87 6.71
TCGAvisualize_EAbarplot 6.55 0.00 7.10
TCGAanalyze_survival 3.37 2.56 6.07
GDCprepare_clinic 3.79 1.60 5.49
TCGAanalyze_EAcomplete 5.23 0.02 5.25
* 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: 3 NOTEs
See
'E:/biocbld/bbs-3.3-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_2.0.13.zip
* DONE (TCGAbiolinks)