Marcel Ramos
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TCGAutils |
| Branch: RELEASE_3_10 |
| Last Commit: 7f5faef |
| Last Changed Date: 2020-01-18 12:45:57 -0400 (Sat, 18 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:30:26 -0400 (Wed, 15 Apr 2020).
| Package 1710/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TCGAutils 1.6.2 Marcel Ramos
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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: 1.6.2 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TCGAutils_1.6.2.tar.gz |
| StartedAt: 2020-04-15 07:03:27 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:17:05 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 818.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAutils.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings TCGAutils_1.6.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/TCGAutils.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.2'
* package encoding: UTF-8
* 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 '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 35.15 2.15 38.22
TCGAprimaryTumors 28.88 3.00 33.80
curatedTCGAData-helpers 20.52 1.23 22.72
imputeAssay 18.31 0.80 19.97
oncoPrintTCGA 15.49 1.02 17.27
trimColData 13.08 2.99 16.80
makeSummarizedExperimentFromGISTIC 5.44 0.63 21.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
simplifyTCGA 57.29 3.52 70.37
TCGAprimaryTumors 31.94 2.03 34.89
trimColData 26.57 0.81 36.93
imputeAssay 26.66 0.70 29.38
oncoPrintTCGA 24.34 0.86 32.87
curatedTCGAData-helpers 23.35 0.81 24.88
makeSummarizedExperimentFromGISTIC 9.55 0.63 30.11
* 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-3.10-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/3.10/bioc/src/contrib/TCGAutils_1.6.2.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.6.2.zip && rm TCGAutils_1.6.2.tar.gz TCGAutils_1.6.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 64208 100 64208 0 0 648k 0 --:--:-- --:--:-- --:--:-- 674k
install for i386
* installing *source* package 'TCGAutils' ...
** using staged installation
** 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
TCGAprimaryTumors html
finding level-2 HTML links ... done
TCGAsampleSelect html
TCGAutils-package html
builds html
clinicalNames html
curatedTCGAData-helpers html
diseaseCodes html
findGRangesCols html
generateMap html
getFileName html
hidden-helpers html
imputeAssay html
makeGRangesListFromCopyNumber html
makeGRangesListFromExonFiles html
makeSummarizedExperimentFromGISTIC html
mergeColData html
oncoPrintTCGA html
sampleTypes html
simplifyTCGA html
trimColData html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'TCGAutils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TCGAutils' as TCGAutils_1.6.2.zip
* DONE (TCGAutils)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TCGAutils' successfully unpacked and MD5 sums checked
|
TCGAutils.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
== testthat results ===========================================================
[ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
12.14 1.23 20.70
|
TCGAutils.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
== testthat results ===========================================================
[ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
16.23 0.70 20.34
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TCGAutils.Rcheck/examples_i386/TCGAutils-Ex.timings
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TCGAutils.Rcheck/examples_x64/TCGAutils-Ex.timings
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