Ning Leng
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/EBSeq |
| Branch: RELEASE_3_8 |
| Last Commit: b431657 |
| Last Changed Date: 2019-01-04 13:30:26 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:53 -0400 (Sat, 13 Apr 2019).
| Package 452/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EBSeq 1.22.1 Ning Leng
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: EBSeq |
| Version: 1.22.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings EBSeq_1.22.1.tar.gz |
| StartedAt: 2019-04-13 01:58:55 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:01:55 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 180.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EBSeq.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EBSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings EBSeq_1.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/EBSeq.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.22.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'plot'
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 plot
qqplot quantile rainbow rbeta rect smoothScatter var
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
"par", "plot", "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
Examples with CPU or elapsed time > 5s
user system elapsed
GetMultiFC 5.75 0.01 5.76
GetMultiPP 5.44 0.00 5.44
EBMultiTest 5.16 0.00 5.15
* 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-3.8-bioc/meat/EBSeq.Rcheck/00check.log'
for details.
EBSeq.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/EBSeq_1.22.1.tar.gz && rm -rf EBSeq.buildbin-libdir && mkdir EBSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EBSeq.buildbin-libdir EBSeq_1.22.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL EBSeq_1.22.1.zip && rm EBSeq_1.22.1.tar.gz EBSeq_1.22.1.zip
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install for i386
* installing *source* package 'EBSeq' ...
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'EBSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EBSeq' as EBSeq_1.22.1.zip
* DONE (EBSeq)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'EBSeq' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
EBSeq.Rcheck/examples_i386/EBSeq-Ex.timings
|
EBSeq.Rcheck/examples_x64/EBSeq-Ex.timings
|