Ning Leng
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/EBSeq |
| git_branch: RELEASE_3_13 |
| git_last_commit: c92c0b9 |
| git_last_commit_date: 2021-05-19 11:59:00 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:03 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the EBSeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EBSeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 551/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EBSeq 1.32.0 (landing page) Ning Leng
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: EBSeq |
| Version: 1.32.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EBSeq_1.32.0.tar.gz |
| StartedAt: 2021-10-14 22:38:20 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:40:21 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 120.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EBSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings EBSeq_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/EBSeq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EBSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EBSeq' version '1.32.0'
* 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 'EBSeq' can be installed ... OK
* 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.
* 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
DenNHist: no visible global function definition for 'hist'
DenNHist: no visible global function definition for 'lines'
DenNHist: no visible global function definition for 'dbeta'
DenNHist: no visible global function definition for 'legend'
EBMultiTest : <anonymous>: no visible global function definition for
'quantile'
EBMultiTest: no visible global function definition for 'quantile'
EBMultiTest : <anonymous>: no visible binding for global variable 'var'
EBMultiTest: no visible binding for global variable 'var'
EBTest : <anonymous>: no visible global function definition for
'quantile'
EBTest: no visible global function definition for 'quantile'
EBTest: no visible binding for global variable 'var'
GetDEResults: no visible binding for global variable 'median'
LogN: no visible global function definition for 'optim'
LogNMulti: no visible global function definition for 'optim'
MedianNorm : <anonymous>: no visible global function definition for
'median'
MedianNorm : <anonymous> : <anonymous>: no visible global function
definition for 'median'
PlotPattern: no visible global function definition for 'par'
PlotPattern: no visible global function definition for 'rainbow'
PlotPattern: no visible global function definition for 'heatmap'
PlotPostVsRawFC: no visible global function definition for 'par'
PlotPostVsRawFC: no visible global function definition for 'abline'
PlotPostVsRawFC: no visible global function definition for 'rect'
PolyFitPlot: no visible global function definition for 'lm'
PolyFitPlot: no visible global function definition for 'smoothScatter'
PolyFitPlot: no visible global function definition for 'axis'
PolyFitPlot: no visible global function definition for 'lines'
QQP: no visible global function definition for 'rbeta'
QQP: no visible global function definition for 'qqplot'
QQP: no visible global function definition for 'lm'
QQP: no visible global function definition for 'abline'
QuantileNorm : <anonymous>: no visible global function definition for
'quantile'
beta.mom: no visible global function definition for 'var'
Undefined global functions or variables:
abline axis dbeta heatmap hist legend lines lm median optim par
qqplot quantile rainbow rbeta rect smoothScatter var
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
"par", "rect", "smoothScatter")
importFrom("stats", "dbeta", "heatmap", "lm", "median", "optim",
"qqplot", "quantile", "rbeta", "var")
to your NAMESPACE file.
* 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 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/EBSeq.Rcheck/00check.log'
for details.
EBSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/EBSeq_1.32.0.tar.gz && rm -rf EBSeq.buildbin-libdir && mkdir EBSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBSeq.buildbin-libdir EBSeq_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL EBSeq_1.32.0.zip && rm EBSeq_1.32.0.tar.gz EBSeq_1.32.0.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 240k 100 240k 0 0 789k 0 --:--:-- --:--:-- --:--:-- 792k
install for i386
* installing *source* package 'EBSeq' ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'EBSeq'
finding HTML links ... done
DenNHist html
EBMultiTest html
EBSeq_NingLeng-package html
EBTest html
GeneMat html
GetDEResults html
GetMultiFC html
GetMultiPP html
GetNg html
GetNormalizedMat html
GetPP html
GetPPMat html
GetPatterns html
IsoList html
IsoMultiList html
Likefun html
LikefunMulti html
LogN html
LogNMulti html
MedianNorm html
MultiGeneMat html
PlotPattern html
PlotPostVsRawFC html
PolyFitPlot html
PostFC html
QQP html
QuantileNorm html
RankNorm html
beta.mom html
crit_fun html
f0 html
f1 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 'EBSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBSeq' as EBSeq_1.32.0.zip
* DONE (EBSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'EBSeq' successfully unpacked and MD5 sums checked
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EBSeq.Rcheck/examples_i386/EBSeq-Ex.timings
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EBSeq.Rcheck/examples_x64/EBSeq-Ex.timings
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