Marcel Ramos
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TCGAutils |
| Branch: RELEASE_3_11 |
| Last Commit: c6301f3 |
| Last Changed Date: 2020-09-14 14:09:15 -0400 (Mon, 14 Sep 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:55 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE TCGAutils PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1786/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TCGAutils 1.8.1 Marcel Ramos
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: TCGAutils |
| Version: 1.8.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TCGAutils_1.8.1.tar.gz |
| StartedAt: 2020-10-17 08:48:16 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 09:02:22 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 845.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TCGAutils.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TCGAutils.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TCGAutils_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TCGAutils.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.8.1'
* 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 (user + system) or elapsed time > 5s
user system elapsed
simplifyTCGA 52.36 2.97 56.71
TCGAprimaryTumors 25.77 2.60 30.19
trimColData 20.43 3.63 25.10
imputeAssay 21.52 0.76 22.98
curatedTCGAData-helpers 20.71 0.89 22.29
oncoPrintTCGA 17.22 1.37 20.38
makeSummarizedExperimentFromGISTIC 6.42 0.50 22.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simplifyTCGA 38.66 2.26 41.82
TCGAprimaryTumors 27.56 1.78 30.30
imputeAssay 21.50 0.82 23.03
trimColData 21.03 0.74 22.61
curatedTCGAData-helpers 20.74 1.01 22.46
oncoPrintTCGA 15.28 0.69 16.49
makeSummarizedExperimentFromGISTIC 6.19 0.48 22.73
* 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-3.11-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://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TCGAutils_1.8.1.tar.gz && rm -rf TCGAutils.buildbin-libdir && mkdir TCGAutils.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TCGAutils.buildbin-libdir TCGAutils_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TCGAutils_1.8.1.zip && rm TCGAutils_1.8.1.tar.gz TCGAutils_1.8.1.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 64597 100 64597 0 0 1142k 0 --:--:-- --:--:-- --:--:-- 1261k
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_1.8.1.zip
* DONE (TCGAutils)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TCGAutils' successfully unpacked and MD5 sums checked
|
TCGAutils.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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
13.79 1.42 21.64
|
TCGAutils.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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
15.70 0.57 21.26
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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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