Marcel Ramos
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TCGAutils |
| Branch: RELEASE_3_8 |
| Last Commit: b8b085b |
| Last Changed Date: 2019-02-13 14:40:03 -0400 (Wed, 13 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:16 -0400 (Sat, 13 Apr 2019).
| Package 1548/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TCGAutils 1.2.2 Marcel Ramos
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | NA | |||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TCGAutils |
| Version: 1.2.2 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TCGAutils_1.2.2.tar.gz |
| StartedAt: 2019-04-13 05:53:19 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 06:02:59 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 580.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAutils.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings TCGAutils_1.2.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/TCGAutils.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TCGAutils/DESCRIPTION' ... OK
* this is package 'TCGAutils' version '1.2.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'TCGAutils' can be installed ... OK
* 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 ... NOTE
Unexported objects imported by ':::' calls:
'BiocGenerics:::replaceSlots' 'GenomicRanges:::.normarg_field'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
simplifyTCGA 34.62 3.86 39.28
qreduceTCGA 36.42 1.97 39.11
imputeAssay 10.37 1.23 12.53
makeSummarizedExperimentFromGISTIC 8.30 0.74 23.97
symbolsToRanges 5.39 1.72 7.14
mirToRanges 5.97 0.69 7.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
simplifyTCGA 25.23 2.46 28.41
qreduceTCGA 23.91 1.83 26.18
makeSummarizedExperimentFromGISTIC 9.50 0.66 24.64
imputeAssay 8.60 1.00 10.17
mirToRanges 7.11 0.64 8.24
symbolsToRanges 5.83 0.20 6.03
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/TCGAutils.Rcheck/00check.log'
for details.
TCGAutils.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/TCGAutils_1.2.2.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.2.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.2.2.zip && rm TCGAutils_1.2.2.tar.gz TCGAutils_1.2.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 53507 100 53507 0 0 1444k 0 --:--:-- --:--:-- --:--:-- 1632k
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* installing *source* package 'TCGAutils' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TCGAutils'
finding HTML links ... done
ID-translation html
TCGAbarcode html
TCGAbiospec html
TCGAsampleSelect html
TCGAutils-package html
finding level-2 HTML links ... done
builds html
clinicalNames html
curatedTCGAData-helpers html
diseaseCodes html
findGRangesCols html
generateMap html
getFileNames html
imputeAssay html
makeGRangesListFromCopyNumber html
makeGRangesListFromExonFiles html
makeSummarizedExperimentFromGISTIC html
mergeColData html
mirToRanges html
qreduceTCGA html
sampleTypes html
simplifyTCGA html
symbolsToRanges html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
Warning in untar2(tarfile, files, list, exdir, restore_times) :
restoring symbolic link as a file copy
* installing *source* package 'TCGAutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAutils' as TCGAutils_1.2.2.zip
* DONE (TCGAutils)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'TCGAutils' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
TCGAutils.Rcheck/tests_i386/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> #library(TCGAutils)
>
> #test_check("TCGAutils")
>
> proc.time()
user system elapsed
0.18 0.04 0.21
|
TCGAutils.Rcheck/tests_x64/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> #library(TCGAutils)
>
> #test_check("TCGAutils")
>
> proc.time()
user system elapsed
0.20 0.01 0.20
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TCGAutils.Rcheck/examples_i386/TCGAutils-Ex.timings
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TCGAutils.Rcheck/examples_x64/TCGAutils-Ex.timings
|