Package: PathwaySplice

Version: 1.6.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PathwaySplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PathwaySplice_1.6.1.tar.gz

StartedAt: 2019-04-13 04:25:23 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 04:44:29 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 1145.4 seconds

RetCode: 0

Status:  OK

CheckDir: PathwaySplice.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PathwaySplice.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings PathwaySplice_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/PathwaySplice.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 'PathwaySplice/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PathwaySplice' version '1.6.1'
* 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'
 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 'PathwaySplice' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
.onAttach: no visible global function definition for 'winMenuAddItem'
compareResults2: no visible global function definition for 'ggplot'
compareResults2: no visible global function definition for 'aes'
compareResults2: no visible binding for global variable
  'random_sampling_200k'
compareResults2: no visible binding for global variable 'PValue'
compareResults2: no visible binding for global variable 'PathwaySplice'
compareResults2: no visible global function definition for 'geom_point'
compareResults2: no visible global function definition for
  'geom_smooth'
compareResults2: no visible global function definition for 'labs'
compareResults2: no visible global function definition for
  'scale_colour_manual'
compareResults2: no visible global function definition for
  'scale_shape_manual'
netplot: no visible global function definition for 'get.col.scale'
Undefined global functions or variables:
  PValue PathwaySplice aes geom_point geom_smooth get.col.scale ggplot
  labs random_sampling_200k scale_colour_manual scale_shape_manual
  winMenuAddItem
Consider adding
  importFrom("utils", "winMenuAddItem")
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
compareResults   46.65   3.42   51.17
enrichmentMap    45.80   2.20   48.16
runPathwaySplice 38.14   0.87   39.10
lrTestBias       15.41   0.71   16.11
makeGeneTable    13.76   0.00   13.78
gmtGene2Cat      10.97   0.22   11.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
enrichmentMap    44.06   2.39   46.54
runPathwaySplice 40.99   2.39   43.50
compareResults   31.44   1.64   33.97
lrTestBias       14.86   0.02   14.88
makeGeneTable    14.03   0.00   14.03
gmtGene2Cat       9.51   0.09    9.73
* 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 ... 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/PathwaySplice.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/PathwaySplice_1.6.1.tar.gz && rm -rf PathwaySplice.buildbin-libdir && mkdir PathwaySplice.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PathwaySplice.buildbin-libdir PathwaySplice_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL PathwaySplice_1.6.1.zip && rm PathwaySplice_1.6.1.tar.gz PathwaySplice_1.6.1.zip
###
##############################################################################
##############################################################################


  % 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 2297k  100 2297k    0     0  33.4M      0 --:--:-- --:--:-- --:--:-- 35.6M

install for i386

* installing *source* package 'PathwaySplice' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PathwaySplice'
    finding HTML links ... done
    compareResults                          html  
    enrichmentMap                           html  
    featureBasedData                        html  
    gmtGene2Cat                             html  
    lrTestBias                              html  
    makeGeneTable                           html  
    outKegg2Gmt                             html  
    runPathwaySplice                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PathwaySplice' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PathwaySplice' as PathwaySplice_1.6.1.zip
* DONE (PathwaySplice)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'PathwaySplice' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("PathwaySplice")
Loading required package: PathwaySplice



[1] "P-value from logistic regression is 3.98e-205"
== testthat results  ===========================================================
OK: 4 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 162.25    5.31  168.65 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("PathwaySplice")
Loading required package: PathwaySplice



[1] "P-value from logistic regression is 3.98e-205"
== testthat results  ===========================================================
OK: 4 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 190.90    8.87  200.86