Koen Van den Berge
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/stageR |
| Branch: RELEASE_3_11 |
| Last Commit: c821d27 |
| Last Changed Date: 2020-04-27 15:11:40 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:52 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE stageR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1739/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| stageR 1.10.0 Koen Van den Berge
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: stageR |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:stageR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings stageR_1.10.0.tar.gz |
| StartedAt: 2020-10-17 08:38:07 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 08:41:37 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 209.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: stageR.Rcheck |
| Warnings: 4 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:stageR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings stageR_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/stageR.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 'stageR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'stageR' version '1.10.0'
* 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 'stageR' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpsVHDsz/R.INSTALL211013686b52/stageR/man/getAdjustedPValues.Rd:34: missing link 'stageWiseAdjustment,stageR,character,numeric-method'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpsVHDsz/R.INSTALL211013686b52/stageR/man/stageRClass.Rd:19: missing link 'getAdjustedPValues,stageR,logical,logical-method'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpsVHDsz/R.INSTALL211013686b52/stageR/man/stageRClass.Rd:19: missing link 'getResults,stageR-method'
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/stageR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
'methods' 'stats'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stageWiseTest : <anonymous>: warning in gsub(x = paste(namesList[ii],
namesListElements[[ii]]), pattern = " ", replace = ":"): partial
argument match of 'replace' to 'replacement'
.stageWiseTest: no visible global function definition for 'p.adjust'
stageR: no visible global function definition for 'new'
stageRTx: no visible global function definition for 'new'
Undefined global functions or variables:
new p.adjust
Consider adding
importFrom("methods", "new")
importFrom("stats", "p.adjust")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getAdjustedPValues.Rd':
'stageWiseAdjustment,stageR,character,numeric-method'
Missing link or links in documentation object 'stageRClass.Rd':
'getAdjustedPValues,stageR,logical,logical-method'
'getResults,stageR-method'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
'stageR' 'stageRTx'
Undocumented S4 methods:
generic 'adjustedAlphaLevel' and siglist 'stageR'
generic 'getAdjustedPValues' and siglist 'stageR,logical,logical'
generic 'getAlpha' and siglist 'stageR'
generic 'getMethod' and siglist 'stageR'
generic 'getPConfirmation' and siglist 'stageR'
generic 'getPScreen' and siglist 'stageR'
generic 'getResults' and siglist 'stageR'
generic 'getSignificantGenes' and siglist 'stageRTx'
generic 'getSignificantTx' and siglist 'stageRTx'
generic 'getTx2gene' and siglist 'stageRTx'
generic 'isAdjusted' and siglist 'stageR'
generic 'isPScreenAdjusted' and siglist 'stageR'
generic 'stageWiseAdjustment' and siglist 'stageR,character,numeric'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'adjustedAlphaLevel'
'...'
Objects in \usage without \alias in documentation object 'adjustedAlphaLevel':
'\S4method{adjustedAlphaLevel}{stageR}'
Objects in \usage without \alias in documentation object 'getAdjustedPValues':
'\S4method{getAdjustedPValues}{stageR,logical,logical}'
Objects in \usage without \alias in documentation object 'getAlpha':
'\S4method{getAlpha}{stageR}'
Objects in \usage without \alias in documentation object 'getMethod':
'\S4method{getMethod}{stageR}'
Undocumented arguments in documentation object 'getPConfirmation'
'...'
Objects in \usage without \alias in documentation object 'getPConfirmation':
'\S4method{getPConfirmation}{stageR}'
Objects in \usage without \alias in documentation object 'getPScreen':
'\S4method{getPScreen}{stageR}'
Undocumented arguments in documentation object 'getResults'
'...'
Objects in \usage without \alias in documentation object 'getResults':
'\S4method{getResults}{stageR}'
Undocumented arguments in documentation object 'getSignificantGenes'
'...'
Objects in \usage without \alias in documentation object 'getSignificantGenes':
'\S4method{getSignificantGenes}{stageRTx}'
Undocumented arguments in documentation object 'getSignificantTx'
'...'
Objects in \usage without \alias in documentation object 'getSignificantTx':
'\S4method{getSignificantTx}{stageRTx}'
Objects in \usage without \alias in documentation object 'getTx2gene':
'\S4method{getTx2gene}{stageRTx}'
Objects in \usage without \alias in documentation object 'isAdjusted':
'\S4method{isAdjusted}{stageR}'
Objects in \usage without \alias in documentation object 'isPScreenAdjusted':
'\S4method{isPScreenAdjusted}{stageR}'
Documented arguments not in \usage in documentation object 'stageR':
'...'
Documented arguments not in \usage in documentation object 'stageRTx':
'...'
Objects in \usage without \alias in documentation object 'stageWiseAdjustment':
'\S4method{stageWiseAdjustment}{stageR,character,numeric}'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
** 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: 4 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/stageR.Rcheck/00check.log'
for details.
stageR.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/stageR_1.10.0.tar.gz && rm -rf stageR.buildbin-libdir && mkdir stageR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=stageR.buildbin-libdir stageR_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL stageR_1.10.0.zip && rm stageR_1.10.0.tar.gz stageR_1.10.0.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 909k 100 909k 0 0 5334k 0 --:--:-- --:--:-- --:--:-- 5547k
install for i386
* installing *source* package 'stageR' ...
** 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 'stageR'
finding HTML links ... done
adjustedAlphaLevel html
esetProstate html
getAdjustedPValues html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpsVHDsz/R.INSTALL211013686b52/stageR/man/getAdjustedPValues.Rd:34: missing link 'stageWiseAdjustment,stageR,character,numeric-method'
getAlpha html
getMethod html
getPConfirmation html
getPScreen html
getResults html
getSignificantGenes html
getSignificantTx html
getTx2gene html
hammer.eset html
isAdjusted html
isPScreenAdjusted html
stageR html
stageRClass html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpsVHDsz/R.INSTALL211013686b52/stageR/man/stageRClass.Rd:19: missing link 'getAdjustedPValues,stageR,logical,logical-method'
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpsVHDsz/R.INSTALL211013686b52/stageR/man/stageRClass.Rd:19: missing link 'getResults,stageR-method'
stageRTx html
stageWiseAdjustment 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 'stageR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'stageR' as stageR_1.10.0.zip
* DONE (stageR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'stageR' successfully unpacked and MD5 sums checked
|
stageR.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(stageR)
Loading required package: SummarizedExperiment
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'stageR'
The following object is masked from 'package:methods':
getMethod
>
> test_check("stageR")
== testthat results ===========================================================
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.87 0.78 8.64
|
stageR.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(stageR)
Loading required package: SummarizedExperiment
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'stageR'
The following object is masked from 'package:methods':
getMethod
>
> test_check("stageR")
== testthat results ===========================================================
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.06 0.29 7.34
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stageR.Rcheck/examples_i386/stageR-Ex.timings
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stageR.Rcheck/examples_x64/stageR-Ex.timings
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