Dongmin Jung
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PPInfer |
| Branch: RELEASE_3_8 |
| Last Commit: 221064e |
| Last Changed Date: 2018-12-18 06:05:31 -0400 (Tue, 18 Dec 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:27:49 -0400 (Sat, 13 Apr 2019).
| Package 1181/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PPInfer 1.8.1 Dongmin Jung
| 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: PPInfer |
| Version: 1.8.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PPInfer_1.8.1.tar.gz |
| StartedAt: 2019-04-13 04:37:53 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:47:04 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 550.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PPInfer.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:PPInfer.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PPInfer_1.8.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/PPInfer.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 'PPInfer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PPInfer' version '1.8.1'
* 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'
NOTE
Depends: includes the non-default packages:
'biomaRt' 'fgsea' 'kernlab' 'ggplot2' 'igraph' 'STRINGdb'
'yeastExpData'
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 'PPInfer' 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
ORA: no visible global function definition for 'txtProgressBar'
ORA: no visible global function definition for 'fisher.test'
ORA: no visible global function definition for 'setTxtProgressBar'
ORA: no visible global function definition for 'p.adjust'
ORA.barplot: no visible global function definition for 'p.adjust'
enrich.net: no visible global function definition for 'stack'
enrich.net: no visible global function definition for 'adjustcolor'
enrich.net : <anonymous>: no visible global function definition for
'adjustcolor'
enrich.net: no visible binding for global variable 'legend'
net.infer: no visible global function definition for 'na.omit'
net.infer.ST: no visible global function definition for 'na.omit'
ppi.infer.human: no visible global function definition for 'na.omit'
ppi.infer.mouse: no visible global function definition for 'na.omit'
Undefined global functions or variables:
adjustcolor fisher.test legend na.omit p.adjust setTxtProgressBar
stack txtProgressBar
Consider adding
importFrom("grDevices", "adjustcolor")
importFrom("graphics", "legend")
importFrom("stats", "fisher.test", "na.omit", "p.adjust")
importFrom("utils", "setTxtProgressBar", "stack", "txtProgressBar")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ppi.infer.human 52.28 1.35 77.72
ppi.infer.mouse 31.97 1.21 43.04
ORA.barplot 0.44 0.02 22.83
ORA 0.12 0.04 22.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ppi.infer.human 42.36 2.04 67.78
ppi.infer.mouse 32.80 1.75 51.17
ORA.barplot 0.44 0.01 22.82
ORA 0.11 0.02 22.48
* 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/PPInfer.Rcheck/00check.log'
for details.
PPInfer.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/PPInfer_1.8.1.tar.gz && rm -rf PPInfer.buildbin-libdir && mkdir PPInfer.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PPInfer.buildbin-libdir PPInfer_1.8.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL PPInfer_1.8.1.zip && rm PPInfer_1.8.1.tar.gz PPInfer_1.8.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'PPInfer' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PPInfer'
finding HTML links ... done
GSEA.barplot html
ORA html
ORA.barplot html
PPInfer-package html
enrich.net html
net.infer html
net.infer.ST html
net.kernel html
ppi.infer.human html
ppi.infer.mouse html
self.train.kernel html
** building package indices
** installing vignettes
'PPInfer.Rnw'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'PPInfer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PPInfer' as PPInfer_1.8.1.zip
* DONE (PPInfer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'PPInfer' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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PPInfer.Rcheck/examples_i386/PPInfer-Ex.timings
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PPInfer.Rcheck/examples_x64/PPInfer-Ex.timings
|