| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:12 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the ReportingTools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReportingTools.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1579/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReportingTools 2.34.0 (landing page) Jason A. Hackney
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ReportingTools |
| Version: 2.34.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReportingTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ReportingTools_2.34.0.tar.gz |
| StartedAt: 2022-04-13 01:29:30 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 01:45:05 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 934.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReportingTools.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReportingTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ReportingTools_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ReportingTools.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ReportingTools/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ReportingTools' version '2.34.0' * 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 'ReportingTools' 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 ... NOTE .GeneSetCollection.to.data.frame: no visible binding for global variable 'description' .GeneSetCollection.to.html: no visible binding for global variable 'description' .GeneSetCollection.to.html2: no visible binding for global variable 'description' .PFAMhyperG.to.html: no visible binding for global variable 'keytype' .PFAMhyperG.to.html: no visible binding for global variable 'columns' .make.gene.plots: no visible global function definition for 'exprs' .marrayLM.to.data.frame: no visible global function definition for 'featureNames' .marrayLM.to.data.frame: no visible global function definition for 'fData' .marrayLM.to.html: no visible global function definition for 'featureNames' .marrayLM.to.html: no visible global function definition for 'fData' check.ids: no visible binding for global variable 'org.Hs.eg.db' check.ids: no visible global function definition for 'keys' custHeaderPanel : <anonymous>: no visible binding for global variable 'tags' custHeaderPanel : <anonymous>: no visible global function definition for 'HTML' custHeaderPanel: no visible global function definition for 'tagList' custHeaderPanel: no visible global function definition for 'tag' custHeaderPanel: no visible global function definition for 'div' custHeaderPanel: no visible global function definition for 'h1' publish,trellis-HTMLReport: no visible binding for global variable 'htmlRep' toReportDF,DESeqDataSet: no visible global function definition for 'mcols' Undefined global functions or variables: HTML columns description div exprs fData featureNames h1 htmlRep keys keytype mcols org.Hs.eg.db tag tagList tags * 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 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... Running 'runTests.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-3.14-bioc/meat/ReportingTools.Rcheck/00check.log' for details.
ReportingTools.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ReportingTools_2.34.0.tar.gz && rm -rf ReportingTools.buildbin-libdir && mkdir ReportingTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReportingTools.buildbin-libdir ReportingTools_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ReportingTools_2.34.0.zip && rm ReportingTools_2.34.0.tar.gz ReportingTools_2.34.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
41 1095k 41 455k 0 0 1202k 0 --:--:-- --:--:-- --:--:-- 1203k
100 1095k 100 1095k 0 0 1530k 0 --:--:-- --:--:-- --:--:-- 1530k
install for i386
* installing *source* package 'ReportingTools' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'objectToHTML' with signature 'object="ggbio"': no definition for class "ggbio"
** help
*** installing help indices
converting help for package 'ReportingTools'
finding HTML links ... done
BaseReportType-class html
CSVFile-class html
CSVFile html
DataPackage-class html
DataPackage html
HTMLReport-class html
HTMLReport html
HTMLReportRef-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/ReportingTools.buildbin-libdir/00LOCK-ReportingTools/00new/ReportingTools/help/HTMLReport.html
Link html
ReportHandlers-class html
addReportColumns-methods html
custHeaderPanel html
filename-methods html
finish-methods html
mockRnaSeqData html
objectToHTML-methods html
publish-methods html
finding level-2 HTML links ... done
readReport html
reporting.theme html
reporting.theme.alternate html
toReportDF-methods html
validConnection 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 'ReportingTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReportingTools' as ReportingTools_2.34.0.zip
* DONE (ReportingTools)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ReportingTools' successfully unpacked and MD5 sums checked
|
ReportingTools.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> require("ReportingTools") || stop("unable to load ReportingTools")
Loading required package: ReportingTools
Loading required package: knitr
[1] TRUE
> BiocGenerics:::testPackage("ReportingTools")
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: org.Hs.eg.db
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
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
The following object is masked from 'package:Biobase':
rowMedians
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: annotate
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: Category
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
<script language="JavaScript" src="jslib/jquery-1.8.0.min.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables-1.9.3.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.columnFilter.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.plugins.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.reprise.js"></script>
<script language="JavaScript" src="jslib/bootstrap.js"></script>
<link rel="stylesheet" type="text/css" href="csslib/bootstrap.css" />
<link rel="stylesheet" type="text/css" href="csslib/reprise.table.bootstrap.css" />
processing file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/ReportingTools/examples/testRmd.Rmd
ordinary text without R code
label: unnamed-chunk-1 (with options)
List of 2
$ message: logi FALSE
$ output : chr "hide"
ordinary text without R code
label: unnamed-chunk-2 (with options)
List of 1
$ results: chr "asis"
ordinary text without R code
label: unnamed-chunk-3 (with options)
List of 1
$ results: chr "asis"
ordinary text without R code
label: unnamed-chunk-4 (with options)
List of 1
$ results: chr "asis"
output file: testRmd.md
Created file named 'testDataPackage/testPkg/man/my.df2.Rd'.
Edit the file and move it to the appropriate directory.
RUNIT TEST PROTOCOL -- Wed Apr 13 01:40:58 2022
***********************************************
Number of test functions: 45
Number of errors: 0
Number of failures: 0
1 Test Suite :
ReportingTools RUnit Tests - 45 test functions, 0 errors, 0 failures
Number of test functions: 45
Number of errors: 0
Number of failures: 0
Warning messages:
1: In DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
2: In DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
>
> proc.time()
user system elapsed
215.21 25.09 256.76
|
ReportingTools.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> require("ReportingTools") || stop("unable to load ReportingTools")
Loading required package: ReportingTools
Loading required package: knitr
[1] TRUE
> BiocGenerics:::testPackage("ReportingTools")
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: org.Hs.eg.db
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
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
The following object is masked from 'package:Biobase':
rowMedians
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: annotate
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: Category
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
<script language="JavaScript" src="jslib/jquery-1.8.0.min.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables-1.9.3.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.columnFilter.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.plugins.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.reprise.js"></script>
<script language="JavaScript" src="jslib/bootstrap.js"></script>
<link rel="stylesheet" type="text/css" href="csslib/bootstrap.css" />
<link rel="stylesheet" type="text/css" href="csslib/reprise.table.bootstrap.css" />
processing file: C:/Users/biocbuild/bbs-3.14-bioc/R/library/ReportingTools/examples/testRmd.Rmd
ordinary text without R code
label: unnamed-chunk-1 (with options)
List of 2
$ message: logi FALSE
$ output : chr "hide"
ordinary text without R code
label: unnamed-chunk-2 (with options)
List of 1
$ results: chr "asis"
ordinary text without R code
label: unnamed-chunk-3 (with options)
List of 1
$ results: chr "asis"
ordinary text without R code
label: unnamed-chunk-4 (with options)
List of 1
$ results: chr "asis"
output file: testRmd.md
Created file named 'testDataPackage/testPkg/man/my.df2.Rd'.
Edit the file and move it to the appropriate directory.
RUNIT TEST PROTOCOL -- Wed Apr 13 01:44:56 2022
***********************************************
Number of test functions: 45
Number of errors: 0
Number of failures: 0
1 Test Suite :
ReportingTools RUnit Tests - 45 test functions, 0 errors, 0 failures
Number of test functions: 45
Number of errors: 0
Number of failures: 0
Warning messages:
1: In DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
2: In DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are characters, converting to factors
>
> proc.time()
user system elapsed
212.20 23.34 237.21
|
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ReportingTools.Rcheck/examples_i386/ReportingTools-Ex.timings
|
ReportingTools.Rcheck/examples_x64/ReportingTools-Ex.timings
|