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CHECK report for RTopper on tokay2

This page was generated on 2018-10-17 08:35:42 -0400 (Wed, 17 Oct 2018).

Package 1294/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTopper 1.26.0
Luigi Marchionni
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RTopper
Branch: RELEASE_3_7
Last Commit: ac4e017
Last Changed Date: 2018-04-30 10:35:21 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RTopper
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTopper.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RTopper_1.26.0.tar.gz
StartedAt: 2018-10-17 04:36:10 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:38:04 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 113.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTopper.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTopper.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RTopper_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/RTopper.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTopper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTopper' version '1.26.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'RTopper' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpiqhkSU/R.INSTALLf7439441b/RTopper/man/fgsList.Rd:37: file link 'org.Hs.eg' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpiqhkSU/R.INSTALLf7439441b/RTopper/man/fgsList.Rd:41: file link 'GO' in package 'GO.db' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpiqhkSU/R.INSTALLf7439441b/RTopper/man/fgsList.Rd:42: file link 'KEGG' in package 'KEGG.db' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/RTopper.Rcheck/00install.out' for details.
* 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:
  'limma'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
computeScore: no visible global function definition for 'glm'
computeScore: no visible global function definition for 'binomial'
computeScore: no visible global function definition for 'AIC'
convertToDr: no visible binding for global variable 'data'
myMean : medianM: no visible binding for global variable 'median'
Undefined global functions or variables:
  AIC binomial data glm median
Consider adding
  importFrom("stats", "AIC", "binomial", "glm", "median")
  importFrom("utils", "data")
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
computeDrStat 13.23   0.17   13.48
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
computeDrStat 15.33   0.03   15.36
* 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/RTopper.Rcheck/00check.log'
for details.



Installation output

RTopper.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/RTopper_1.26.0.tar.gz && rm -rf RTopper.buildbin-libdir && mkdir RTopper.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTopper.buildbin-libdir RTopper_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RTopper_1.26.0.zip && rm RTopper_1.26.0.tar.gz RTopper_1.26.0.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 1094k  100 1094k    0     0  16.7M      0 --:--:-- --:--:-- --:--:-- 18.7M

install for i386

* installing *source* package 'RTopper' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTopper'
    finding HTML links ... done
    RTopper-package                         html  
    adjustPvalGSE                           html  
    finding level-2 HTML links ... done

    combineGSE                              html  
    computeDrStat                           html  
    convertToDr                             html  
    dat                                     html  
    fgsList                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpiqhkSU/R.INSTALLf7439441b/RTopper/man/fgsList.Rd:37: file link 'org.Hs.eg' in package 'org.Hs.eg.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpiqhkSU/R.INSTALLf7439441b/RTopper/man/fgsList.Rd:41: file link 'GO' in package 'GO.db' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpiqhkSU/R.INSTALLf7439441b/RTopper/man/fgsList.Rd:42: file link 'KEGG' in package 'KEGG.db' does not exist and so has been treated as a topic
    gseResultsSep                           html  
    intScores                               html  
    pheno                                   html  
    runBatchGSE                             html  
    sepScores                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RTopper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTopper' as RTopper_1.26.0.zip
* DONE (RTopper)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'RTopper' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

RTopper.Rcheck/examples_i386/RTopper-Ex.timings

nameusersystemelapsed
adjustPvalGSE0.050.000.04
combineGSE0.020.000.02
computeDrStat13.23 0.1713.48
convertToDr3.540.003.55
dat0.130.000.12
fgsList0.030.000.05
gseResultsSep0.030.000.03
intScores0.020.000.03
pheno0.180.000.19
runBatchGSE0.100.020.12
sepScores0.010.010.03

RTopper.Rcheck/examples_x64/RTopper-Ex.timings

nameusersystemelapsed
adjustPvalGSE0.020.010.03
combineGSE000
computeDrStat15.33 0.0315.36
convertToDr4.280.004.29
dat0.110.000.10
fgsList0.020.000.02
gseResultsSep0.010.000.02
intScores0.000.020.01
pheno0.110.000.11
runBatchGSE0.050.010.06
sepScores0.000.020.02