PPInfer 1.2.4
Dongmin Jung
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/PPInfer | | Branch: RELEASE_3_5 | | Last Commit: 8afb8be | | Last Changed Date: 2017-10-12 23:27:22 -0400 (Thu, 12 Oct 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | ERROR | OK | |
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### Running command:
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### rm -rf PPInfer.buildbin-libdir PPInfer.Rcheck && mkdir PPInfer.buildbin-libdir PPInfer.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PPInfer.buildbin-libdir PPInfer_1.2.4.tar.gz >PPInfer.Rcheck\00install.out 2>&1 && cp PPInfer.Rcheck\00install.out PPInfer-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=PPInfer.buildbin-libdir --install="check:PPInfer-install.out" --force-multiarch --no-vignettes --timings PPInfer_1.2.4.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/PPInfer.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.2.4'
* checking package namespace information ... OK
* checking package dependencies ... 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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.dotplot: 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 63.97 1.46 72.69
ppi.infer.mouse 54.58 1.13 65.24
ORA.dotplot 1.48 0.01 23.89
ORA 0.27 0.04 22.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
ppi.infer.human 81.08 2.24 89.82
ppi.infer.mouse 56.72 1.86 65.97
net.infer 4.79 0.07 5.03
ORA.dotplot 1.99 0.05 24.41
ORA 0.22 0.05 22.66
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'httr'
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/PPInfer.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'PPInfer' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'PPInfer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PPInfer' as PPInfer_1.2.4.zip
* DONE (PPInfer)