Christopher Bolen
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/qusage |
| Branch: RELEASE_3_10 |
| Last Commit: 81a68e6 |
| Last Changed Date: 2019-10-29 13:08:46 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:22:04 -0400 (Wed, 15 Apr 2020).
| Package 1355/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qusage 2.20.0 Christopher Bolen
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: qusage |
| Version: 2.20.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qusage.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings qusage_2.20.0.tar.gz |
| StartedAt: 2020-04-15 05:50:16 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:52:56 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 159.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: qusage.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qusage.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings qusage_2.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/qusage.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 'qusage/DESCRIPTION' ... OK
* this is package 'qusage' version '2.20.0'
* 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 'qusage' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/qusage/man/calcVIF.Rd:12: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/qusage/man/makeComparison.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/qusage/man/qgen.Rd:21: file link 'corStruct' in package 'nlme' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/qusage/man/qusage.Rd:12: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/qusage.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
data 8.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
absoluteTest : <anonymous>: no visible global function definition for
'pchisq'
absoluteTest.genePvals: no visible global function definition for 'qt'
absoluteTest.genePvals: no visible global function definition for
'approx'
absoluteTest.genePvals: no visible global function definition for 'dt'
absoluteTest.genePvals: no visible global function definition for
'pnorm'
absoluteTest.genePvals: no visible global function definition for 'pt'
absoluteTest.genePvalsFAST : <anonymous>: no visible global function
definition for 'pt'
aggregateGeneSet: no visible global function definition for 'qt'
aggregateGeneSet : <anonymous>: no visible global function definition
for 'dt'
calcPCor: no visible global function definition for 'model.matrix'
calcPCor: no visible global function definition for 'formula'
calcPCor : <anonymous>: no visible global function definition for 'cov'
calcVIF: no visible global function definition for 'model.matrix'
calcVIF: no visible global function definition for 'formula'
calcVIF : <anonymous>: no visible global function definition for 'cov'
combinePDFs : <anonymous> : <anonymous>: no visible global function
definition for 'approx'
combinePDFs : <anonymous>: no visible global function definition for
'approx'
compareTwoDistsFaster: no visible global function definition for
'runif'
getExAbs: no visible global function definition for 'approx'
homogeneityScore : <anonymous>: no visible global function definition
for 'pchisq'
makeComparison: no visible global function definition for
'model.matrix'
makeComparison: no visible global function definition for 'formula'
multi_conv : <anonymous>: no visible global function definition for
'fft'
multi_conv: no visible global function definition for 'fft'
plotCIs: no visible global function definition for 'p.adjust'
plotCIs: no visible global function definition for 'par'
plotCIs: no visible global function definition for 'rgb'
plotCIs: no visible global function definition for 'abline'
plotCIs: no visible global function definition for 'gray'
plotCIs: no visible global function definition for 'axis'
plotCIs: no visible global function definition for 'text'
plotCIs: no visible global function definition for 'arrows'
plotCIs: no visible global function definition for 'points'
plotCIs: no visible global function definition for 'strwidth'
plotCIs: no visible global function definition for 'strheight'
plotCIs: no visible global function definition for 'polygon'
plotCIs: no visible global function definition for 'box'
plotCIsGenes : <anonymous>: no visible global function definition for
'qt'
plotCIsGenes: no visible global function definition for 'dt'
plotCIsGenes: no visible global function definition for 'par'
plotCIsGenes: no visible global function definition for 'abline'
plotCIsGenes: no visible global function definition for 'gray'
plotCIsGenes: no visible global function definition for 'polygon'
plotCIsGenes: no visible global function definition for 'grey'
plotCIsGenes: no visible global function definition for 'points'
plotCIsGenes: no visible global function definition for 'arrows'
plotCIsGenes: no visible global function definition for 'axis'
plotCIsGenes: no visible global function definition for 'text'
plotCIsGenes: no visible global function definition for 'box'
plotCombinedPDF: no visible global function definition for 'par'
plotCombinedPDF: no visible global function definition for 'abline'
plotCombinedPDF: no visible global function definition for 'lines'
plotDensityCurves: no visible global function definition for 'par'
plotDensityCurves: no visible global function definition for 'abline'
plotDensityCurves: no visible global function definition for 'lines'
plotGeneSetDistributions: no visible global function definition for
'layout'
plotGeneSetDistributions: no visible global function definition for
'par'
plotGeneSetDistributions: no visible global function definition for
'frame'
plotGeneSetDistributions: no visible global function definition for
'text'
plotGeneSetDistributions: no visible global function definition for
'axis'
plotGeneSetDistributions: no visible global function definition for
'dt'
plotGeneSetDistributions: no visible global function definition for
'quantile'
plotGeneSetDistributions: no visible global function definition for
'rect'
plotGeneSetDistributions: no visible global function definition for
'col2rgb'
plotGeneSetDistributions: no visible global function definition for
'rainbow'
plotGeneSetDistributions: no visible global function definition for
'colorRamp'
plotGeneSetDistributions: no visible global function definition for
'rgb'
plotGeneSetDistributions: no visible global function definition for
'approx'
plotGeneSetDistributions: no visible global function definition for
'lines'
plotGeneSetDistributions: no visible global function definition for
'abline'
qgen: no visible global function definition for 'median'
qgen: no visible global function definition for 'model.matrix'
qgen: no visible global function definition for 'formula'
qgen: no visible global function definition for 'residuals'
qgen: no visible global function definition for 'lm'
qgen: no visible global function definition for 'setNames'
qsTable: no visible global function definition for 'p.adjust'
twoCurve.pVal : <anonymous>: no visible global function definition for
'approx'
weighted_conv: no visible global function definition for 'approx'
weighted_conv: no visible global function definition for 'convolve'
Undefined global functions or variables:
abline approx arrows axis box col2rgb colorRamp convolve cov dt fft
formula frame gray grey layout lines lm median model.matrix p.adjust
par pchisq pnorm points polygon pt qt quantile rainbow rect residuals
rgb runif setNames strheight strwidth text
Consider adding
importFrom("grDevices", "col2rgb", "colorRamp", "gray", "grey",
"rainbow", "rgb")
importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
"layout", "lines", "par", "points", "polygon", "rect",
"strheight", "strwidth", "text")
importFrom("stats", "approx", "convolve", "cov", "dt", "fft",
"formula", "lm", "median", "model.matrix", "p.adjust",
"pchisq", "pnorm", "pt", "qt", "quantile", "residuals",
"runif", "setNames")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: GeneSets.Rd:20: Dropping empty section \format
* 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
qgen 20.75 0.29 21.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qgen 19.03 0.17 19.2
* 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 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/qusage.Rcheck/00check.log'
for details.
qusage.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/qusage_2.20.0.tar.gz && rm -rf qusage.buildbin-libdir && mkdir qusage.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qusage.buildbin-libdir qusage_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL qusage_2.20.0.zip && rm qusage_2.20.0.tar.gz qusage_2.20.0.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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 8777k 100 8777k 0 0 53.0M 0 --:--:-- --:--:-- --:--:-- 53.9M
install for i386
* installing *source* package 'qusage' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'qusage'
finding HTML links ... done
GeneSets html
QSarray-class html
aggregateGeneSet html
calcBayesCI html
calcVIF html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/qusage/man/calcVIF.Rd:12: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
combinePDFs html
eset.full html
fluVaccine html
getXcoords html
makeComparison html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/qusage/man/makeComparison.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
newQSarray html
pVal html
plotCIs html
plotCIsGenes html
plotCombinedPDF html
plotDensityCurves html
plotGeneSetDistributions html
qgen html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/qusage/man/qgen.Rd:21: file link 'corStruct' in package 'nlme' does not exist and so has been treated as a topic
qsTable html
qusage html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpeIDA3A/R.INSTALL8d46b887137/qusage/man/qusage.Rd:12: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
read.gmt 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 'qusage' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qusage' as qusage_2.20.0.zip
* DONE (qusage)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'qusage' successfully unpacked and MD5 sums checked
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qusage.Rcheck/examples_i386/qusage-Ex.timings
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qusage.Rcheck/examples_x64/qusage-Ex.timings
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