Vince Carey
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/pathRender |
| Branch: master |
| Last Commit: 53c9e58 |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:54:44 -0400 (Tue, 09 Apr 2019).
| Package 1153/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pathRender 1.51.0 Vince Carey
| 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: pathRender |
| Version: 1.51.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathRender.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pathRender_1.51.0.tar.gz |
| StartedAt: 2019-04-09 04:47:46 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:49:47 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 120.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathRender.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:pathRender.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings pathRender_1.51.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/pathRender.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pathRender/DESCRIPTION' ... OK
* this is package 'pathRender' version '1.51.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'graph', 'Rgraphviz', 'RColorBrewer', 'cMAP', 'AnnotationDbi',
'stats4'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'pathRender' 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
graphcMAP: no visible binding for global variable 'cMAPKEGGPATHWAY'
graphcMAP: no visible binding for global variable 'cMAPCARTAPATHWAY'
graphcMAP: no visible binding for global variable 'cMAPKEGGINTERACTION'
graphcMAP: no visible binding for global variable 'cMAPKEGGMOLECULE'
graphcMAP: no visible binding for global variable
'cMAPCARTAINTERACTION'
graphcMAP: no visible binding for global variable 'cMAPCARTAMOLECULE'
plotExGraph: no visible global function definition for
'colorRampPalette'
plotExGraph: no visible global function definition for 'exprs'
quantizeByRow : <anonymous>: no visible global function definition for
'quantile'
quantizeByRow: no visible global function definition for 'featureNames'
quantizeByRow: no visible global function definition for 'exprs<-'
quantizeByRow: no visible global function definition for 'exprs'
quantizeByRow: no visible global function definition for
'featureNames<-'
reduceES: no visible global function definition for 'na.omit'
reduceES: no visible global function definition for 'featureData<-'
reduceES: no visible global function definition for 'exprs'
reduceES: no visible global function definition for 'phenoData'
rendercMAPPathway: no visible binding for global variable
'cMAPKEGGPATHWAY'
rendercMAPPathway: no visible binding for global variable
'cMAPCARTAPATHWAY'
rendercMAPPathway: no visible binding for global variable
'cMAPKEGGINTERACTION'
rendercMAPPathway: no visible binding for global variable
'cMAPKEGGMOLECULE'
rendercMAPPathway: no visible binding for global variable
'cMAPCARTAINTERACTION'
rendercMAPPathway: no visible binding for global variable
'cMAPCARTAMOLECULE'
plot,coloredGraph-ANY: no visible global function definition for
'palette'
Undefined global functions or variables:
cMAPCARTAINTERACTION cMAPCARTAMOLECULE cMAPCARTAPATHWAY
cMAPKEGGINTERACTION cMAPKEGGMOLECULE cMAPKEGGPATHWAY colorRampPalette
exprs exprs<- featureData<- featureNames featureNames<- na.omit
palette phenoData quantile
Consider adding
importFrom("grDevices", "colorRampPalette", "palette")
importFrom("stats", "na.omit", "quantile")
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 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/pathRender.Rcheck/00check.log'
for details.
pathRender.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/pathRender_1.51.0.tar.gz && rm -rf pathRender.buildbin-libdir && mkdir pathRender.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathRender.buildbin-libdir pathRender_1.51.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL pathRender_1.51.0.zip && rm pathRender_1.51.0.tar.gz pathRender_1.51.0.zip
###
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install for i386
* installing *source* package 'pathRender' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'pathRender'
finding HTML links ... done
colorNodes html
coloredGraph-class html
graphcMAP html
plotExGraph html
pwayGraph-class html
reduceES html
rendercMAP 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 'pathRender' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathRender' as pathRender_1.51.0.zip
* DONE (pathRender)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'pathRender' successfully unpacked and MD5 sums checked
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pathRender.Rcheck/examples_i386/pathRender-Ex.timings
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pathRender.Rcheck/examples_x64/pathRender-Ex.timings
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