Marcel Ramos
| Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021) |
| URL: https://git.bioconductor.org/packages/curatedTCGAData |
| Branch: master |
| Last Commit: 8316294 |
| Last Changed Date: 2021-01-20 15:34:17 -0500 (Wed, 20 Jan 2021) |
| Back to Multiple platform build/check report for BioC 3.13 experimental data |
|
This page was generated on 2021-01-21 16:01:27 -0500 (Thu, 21 Jan 2021).
| TO THE DEVELOPERS/MAINTAINERS OF THE curatedTCGAData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 87/386 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| curatedTCGAData 1.13.5 Marcel Ramos
| malbec2 | Linux (Ubuntu 20.04.1 LTS) / x86_64 | OK | OK | OK | | |||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | [ OK ] |
| Package: curatedTCGAData |
| Version: 1.13.5 |
| Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:curatedTCGAData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings curatedTCGAData_1.13.5.tar.gz |
| StartedAt: 2021-01-21 11:18:09 -0500 (Thu, 21 Jan 2021) |
| EndedAt: 2021-01-21 11:21:02 -0500 (Thu, 21 Jan 2021) |
| EllapsedTime: 172.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: curatedTCGAData.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:curatedTCGAData.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings curatedTCGAData_1.13.5.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/curatedTCGAData.Rcheck' * using R Under development (unstable) (2020-12-30 r79736) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'curatedTCGAData/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'curatedTCGAData' version '1.13.5' * 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 'curatedTCGAData' 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 ... OK * 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 R/sysdata.rda ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * 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: OK
curatedTCGAData.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/curatedTCGAData_1.13.5.tar.gz && rm -rf curatedTCGAData.buildbin-libdir && mkdir curatedTCGAData.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=curatedTCGAData.buildbin-libdir curatedTCGAData_1.13.5.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL curatedTCGAData_1.13.5.zip && rm curatedTCGAData_1.13.5.tar.gz curatedTCGAData_1.13.5.zip
###
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install for i386
* installing *source* package 'curatedTCGAData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'curatedTCGAData'
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finding level-2 HTML links ... done
** 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 'curatedTCGAData' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'curatedTCGAData' as curatedTCGAData_1.13.5.zip
* DONE (curatedTCGAData)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'curatedTCGAData' successfully unpacked and MD5 sums checked
|
curatedTCGAData.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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(curatedTCGAData)
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
>
> test_check("curatedTCGAData")
== Warnings ====================================================================
-- Warning (???): localHub is used when no internet available ------------------
[experimenthub.bioconductor.org] timeout, localHub=TRUE
Backtrace:
1. testthat::expect_true(.test_eh())
4. curatedTCGAData:::.test_eh()
5. base::tryCatch(...)
6. base:::tryCatchList(expr, classes, parentenv, handlers)
7. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. value[[3L]](cond)
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
6.75 1.04 8.39
|
curatedTCGAData.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
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(curatedTCGAData)
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
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Welcome to Bioconductor
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>
> test_check("curatedTCGAData")
== Warnings ====================================================================
-- Warning (???): localHub is used when no internet available ------------------
[experimenthub.bioconductor.org] timeout, localHub=TRUE
Backtrace:
1. testthat::expect_true(.test_eh())
4. curatedTCGAData:::.test_eh()
5. base::tryCatch(...)
6. base:::tryCatchList(expr, classes, parentenv, handlers)
7. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. value[[3L]](cond)
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 3 ]
>
> proc.time()
user system elapsed
7.79 0.98 9.26
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curatedTCGAData.Rcheck/examples_i386/curatedTCGAData-Ex.timings
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curatedTCGAData.Rcheck/examples_x64/curatedTCGAData-Ex.timings
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