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CHECK report for SPIA on tokay1

This page was generated on 2019-04-13 11:20:54 -0400 (Sat, 13 Apr 2019).

Package 1487/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPIA 2.34.0
Adi Laurentiu Tarca
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/SPIA
Branch: RELEASE_3_8
Last Commit: febbfe2
Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SPIA
Version: 2.34.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPIA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SPIA_2.34.0.tar.gz
StartedAt: 2019-04-13 05:41:51 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:53:35 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 703.7 seconds
RetCode: 0
Status:  OK  
CheckDir: SPIA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SPIA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings SPIA_2.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/SPIA.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 'SPIA/DESCRIPTION' ... OK
* this is package 'SPIA' version '2.34.0'
* 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 'SPIA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'graphics'
A package should be listed in only one of these fields.
* 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: 'KEGGgraph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
combfunc: no visible global function definition for 'na.omit'
combfunc: no visible global function definition for 'pnorm'
combfunc: no visible global function definition for 'qnorm'
getP2: no visible global function definition for 'qchisq'
getP2: no visible global function definition for 'pnorm'
getP2: no visible global function definition for 'qnorm'
makeSPIAdata: no visible global function definition for 'parseKGML'
makeSPIAdata: no visible global function definition for 'nodes'
makeSPIAdata: no visible global function definition for 'na.omit'
makeSPIAdata: no visible global function definition for 'edges'
plotP: no visible global function definition for 'na.omit'
plotP: no visible global function definition for 'pnorm'
plotP: no visible global function definition for 'qnorm'
plotP: no visible global function definition for 'text'
spia: no visible global function definition for 'pdf'
spia: no visible global function definition for 'par'
spia: no visible global function definition for 'phyper'
spia: no visible global function definition for 'median'
spia: no visible global function definition for 'sd'
spia: no visible global function definition for 'density'
spia: no visible global function definition for 'dev.off'
spia: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  density dev.off edges median na.omit nodes p.adjust par parseKGML pdf
  phyper pnorm qchisq qnorm sd text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "text")
  importFrom("stats", "density", "median", "na.omit", "p.adjust",
             "phyper", "pnorm", "qchisq", "qnorm", "sd")
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
Examples with CPU or elapsed time > 5s
        user system elapsed
spia  276.96   2.58  279.55
plotP  57.27   1.74   59.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
spia  210.32   2.66  212.99
plotP  43.53   0.89   44.42
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/SPIA.Rcheck/00check.log'
for details.



Installation output

SPIA.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/SPIA_2.34.0.tar.gz && rm -rf SPIA.buildbin-libdir && mkdir SPIA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SPIA.buildbin-libdir SPIA_2.34.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL SPIA_2.34.0.zip && rm SPIA_2.34.0.tar.gz SPIA_2.34.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2332k  100 2332k    0     0  36.4M      0 --:--:-- --:--:-- --:--:-- 38.6M

install for i386

* installing *source* package 'SPIA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SPIA'
    finding HTML links ... done
    SPIA-internal                           html  
    Vessels                                 html  
    colorectalcancer                        html  
    combfunc                                html  
    makeSPIAdata                            html  
    plotP                                   html  
    spia                                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SPIA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SPIA' as SPIA_2.34.0.zip
* DONE (SPIA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'SPIA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

SPIA.Rcheck/examples_i386/SPIA-Ex.timings

nameusersystemelapsed
combfunc000
makeSPIAdata4.730.014.85
plotP57.27 1.7459.09
spia276.96 2.58279.55

SPIA.Rcheck/examples_x64/SPIA-Ex.timings

nameusersystemelapsed
combfunc000
makeSPIAdata3.690.053.74
plotP43.53 0.8944.42
spia210.32 2.66212.99