Josep Gregori
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/msmsEDA |
| Branch: RELEASE_3_9 |
| Last Commit: 145009c |
| Last Changed Date: 2019-05-02 11:53:44 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:28:16 -0400 (Wed, 16 Oct 2019).
| Package 1053/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| msmsEDA 1.22.0 Josep Gregori
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: msmsEDA |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:msmsEDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings msmsEDA_1.22.0.tar.gz |
| StartedAt: 2019-10-16 05:24:37 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:27:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 148.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: msmsEDA.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:msmsEDA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings msmsEDA_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/msmsEDA.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'msmsEDA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msmsEDA' version '1.22.0'
* package encoding: latin1
* 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 'msmsEDA' 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 ... NOTE
Package in Depends field not imported from: 'MSnbase'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'MSnbase:::logging'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
batch.neutralize: no visible global function definition for
'model.matrix'
count.stats: no visible global function definition for 'exprs'
count.stats: no visible binding for global variable 'fivenum'
counts.hc: no visible global function definition for 'exprs'
counts.hc: no visible global function definition for 'hclust'
counts.hc: no visible global function definition for 'dist'
counts.hc: no visible global function definition for 'par'
counts.hc: no visible global function definition for 'pData'
counts.hc: no visible global function definition for 'as.dendrogram'
counts.hc: no visible global function definition for 'dendrapply'
counts.hc: no visible global function definition for 'plot'
counts.hc: no visible global function definition for 'title'
counts.heatmap: no visible global function definition for 'exprs'
counts.heatmap: no visible global function definition for 'pdf'
counts.heatmap: no visible global function definition for 'heatmap'
counts.heatmap: no visible global function definition for 'dev.off'
counts.pca: no visible global function definition for 'exprs'
counts.pca: no visible global function definition for 'prcomp'
counts.pca: no visible global function definition for 'pData'
counts.pca: no visible global function definition for 'text'
counts.pca: no visible global function definition for 'abline'
counts.pca: no visible global function definition for 'title'
disp.estimates: no visible global function definition for 'exprs'
disp.estimates: no visible global function definition for 'pData'
disp.estimates: no visible global function definition for 'pdf'
disp.estimates: no visible global function definition for 'par'
disp.estimates: no visible global function definition for 'quantile'
disp.estimates: no visible global function definition for 'plot'
disp.estimates: no visible global function definition for 'density'
disp.estimates: no visible global function definition for 'abline'
disp.estimates: no visible global function definition for 'title'
disp.estimates: no visible global function definition for 'dev.off'
edgeCol: no visible global function definition for 'is.leaf'
filter.flags: no visible binding for global variable 'var'
filter.flags: no visible global function definition for 'quantile'
norm.counts: no visible global function definition for 'exprs'
norm.counts: no visible global function definition for 'exprs<-'
pp.msms.data: no visible global function definition for 'exprs'
pp.msms.data: no visible global function definition for 'exprs<-'
residual.var : ss: no visible global function definition for 'var'
spc.barplots: no visible global function definition for 'median'
spc.barplots: no visible global function definition for 'par'
spc.barplots: no visible global function definition for 'barplot'
spc.barplots: no visible global function definition for 'abline'
spc.boxplots: no visible global function definition for 'par'
spc.boxplots: no visible global function definition for 'boxplot'
spc.boxplots: no visible global function definition for 'axis'
spc.boxplots: no visible global function definition for 'legend'
spc.densityplots: no visible global function definition for 'density'
spc.densityplots: no visible global function definition for 'par'
spc.densityplots: no visible global function definition for 'plot'
spc.densityplots: no visible global function definition for 'abline'
spc.densityplots: no visible global function definition for 'lines'
spc.densityplots: no visible global function definition for 'legend'
spc.scatterplot: no visible global function definition for 'par'
spc.scatterplot: no visible global function definition for 'plot'
spc.scatterplot: no visible global function definition for 'points'
spc.scatterplot: no visible global function definition for 'abline'
Undefined global functions or variables:
abline as.dendrogram axis barplot boxplot dendrapply density dev.off
dist exprs exprs<- fivenum hclust heatmap is.leaf legend lines median
model.matrix pData par pdf plot points prcomp quantile text title var
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "abline", "axis", "barplot", "boxplot",
"legend", "lines", "par", "plot", "points", "text", "title")
importFrom("stats", "as.dendrogram", "dendrapply", "density", "dist",
"fivenum", "hclust", "heatmap", "is.leaf", "median",
"model.matrix", "prcomp", "quantile", "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-3.9-bioc/meat/msmsEDA.Rcheck/00check.log'
for details.
msmsEDA.Rcheck/00install.out
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### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/msmsEDA_1.22.0.tar.gz && rm -rf msmsEDA.buildbin-libdir && mkdir msmsEDA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=msmsEDA.buildbin-libdir msmsEDA_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL msmsEDA_1.22.0.zip && rm msmsEDA_1.22.0.tar.gz msmsEDA_1.22.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'msmsEDA' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'msmsEDA'
finding HTML links ... done
batch.neutralize html
finding level-2 HTML links ... done
count.stats html
counts.hc html
counts.heatmap html
counts.pca html
disp.estimates html
filter.flags html
gene.table html
msms.dataset html
msmsEDA-package html
norm.counts html
pnms html
pp.msms.data html
spc.barplots html
spc.boxplots html
spc.densityplots html
spc.scatterplot 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 'msmsEDA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msmsEDA' as msmsEDA_1.22.0.zip
* DONE (msmsEDA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'msmsEDA' successfully unpacked and MD5 sums checked
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msmsEDA.Rcheck/examples_i386/msmsEDA-Ex.timings
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msmsEDA.Rcheck/examples_x64/msmsEDA-Ex.timings
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