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CHECK report for CexoR on tokay1

This page was generated on 2020-10-25 12:06:20 -0400 (Sun, 25 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CexoR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 264/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CexoR 1.27.1
Pedro Madrigal
Snapshot Date: 2020-10-24 14:40:19 -0400 (Sat, 24 Oct 2020)
URL: https://git.bioconductor.org/packages/CexoR
Branch: master
Last Commit: a9b251d
Last Changed Date: 2020-06-30 07:24:53 -0400 (Tue, 30 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CexoR
Version: 1.27.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CexoR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CexoR_1.27.1.tar.gz
StartedAt: 2020-10-25 01:07:50 -0400 (Sun, 25 Oct 2020)
EndedAt: 2020-10-25 01:15:26 -0400 (Sun, 25 Oct 2020)
EllapsedTime: 455.1 seconds
RetCode: 0
Status:  OK  
CheckDir: CexoR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CexoR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CexoR_1.27.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CexoR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CexoR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CexoR' version '1.27.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'CexoR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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
cexor: no visible global function definition for 'subsetByOverlaps'
cexor : Stouffer.test: no visible global function definition for
  'qnorm'
cexor : Stouffer.test: no visible global function definition for
  'pnorm'
cexor : Fisher.test: no visible global function definition for 'pchisq'
plotcexor: no visible global function definition for 'colorRampPalette'
plotcexor: no visible global function definition for 'par'
plotcexor: no visible global function definition for 'points'
plotcexor: no visible global function definition for 'abline'
plotcexor: no visible global function definition for 'legend'
pskellam: no visible global function definition for 'pchisq'
pskellam.sp: no visible global function definition for 'pnorm'
pskellam.sp: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  abline colorRampPalette dnorm legend par pchisq pnorm points qnorm
  subsetByOverlaps
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "legend", "par", "points")
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qnorm")
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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
CexoR-package 12.33   0.39   45.84
cexor         12.31   0.08   12.40
plotcexor     11.34   0.11   11.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
CexoR-package 12.78   0.11   13.03
cexor         12.09   0.09   12.19
plotcexor     10.98   0.07   11.05
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/CexoR.Rcheck/00check.log'
for details.



Installation output

CexoR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CexoR_1.27.1.tar.gz && rm -rf CexoR.buildbin-libdir && mkdir CexoR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CexoR.buildbin-libdir CexoR_1.27.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CexoR_1.27.1.zip && rm CexoR_1.27.1.tar.gz CexoR_1.27.1.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 1521k  100 1521k    0     0  24.3M      0 --:--:-- --:--:-- --:--:-- 26.0M

install for i386

* installing *source* package 'CexoR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CexoR'
    finding HTML links ... done
    CexoR-internal                          html  
    CexoR-package                           html  
    cexor                                   html  
    plotcexor                               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 'CexoR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CexoR' as CexoR_1.27.1.zip
* DONE (CexoR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CexoR' successfully unpacked and MD5 sums checked

Tests output

CexoR.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> require("CexoR") || stop("unable to load CexoR")
Loading required package: CexoR
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

[1] TRUE
> BiocGenerics:::testPackage("CexoR")


RUNIT TEST PROTOCOL -- Sun Oct 25 01:14:59 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CexoR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  20.56    1.25   21.81 

CexoR.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> require("CexoR") || stop("unable to load CexoR")
Loading required package: CexoR
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

[1] TRUE
> BiocGenerics:::testPackage("CexoR")


RUNIT TEST PROTOCOL -- Sun Oct 25 01:15:20 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CexoR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  20.18    0.53   20.70 

Example timings

CexoR.Rcheck/examples_i386/CexoR-Ex.timings

nameusersystemelapsed
CexoR-package12.33 0.3945.84
cexor12.31 0.0812.40
plotcexor11.34 0.1111.45

CexoR.Rcheck/examples_x64/CexoR-Ex.timings

nameusersystemelapsed
CexoR-package12.78 0.1113.03
cexor12.09 0.0912.19
plotcexor10.98 0.0711.05