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CHECK report for InterMineR on tokay1

This page was generated on 2018-04-12 13:30:25 -0400 (Thu, 12 Apr 2018).

Package 704/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InterMineR 1.0.0
InterMine Team
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/InterMineR
Branch: RELEASE_3_6
Last Commit: e37bc79
Last Changed Date: 2017-10-30 12:41:42 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: InterMineR
Version: 1.0.0
Command: rm -rf InterMineR.buildbin-libdir InterMineR.Rcheck && mkdir InterMineR.buildbin-libdir InterMineR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InterMineR.buildbin-libdir InterMineR_1.0.0.tar.gz >InterMineR.Rcheck\00install.out 2>&1 && cp InterMineR.Rcheck\00install.out InterMineR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=InterMineR.buildbin-libdir --install="check:InterMineR-install.out" --force-multiarch --no-vignettes --timings InterMineR_1.0.0.tar.gz
StartedAt: 2018-04-12 00:51:28 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:58:11 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 403.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: InterMineR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf InterMineR.buildbin-libdir InterMineR.Rcheck && mkdir InterMineR.buildbin-libdir InterMineR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=InterMineR.buildbin-libdir InterMineR_1.0.0.tar.gz >InterMineR.Rcheck\00install.out 2>&1 && cp InterMineR.Rcheck\00install.out InterMineR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=InterMineR.buildbin-libdir --install="check:InterMineR-install.out" --force-multiarch --no-vignettes --timings InterMineR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/InterMineR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'InterMineR/DESCRIPTION' ... OK
* this is package 'InterMineR' version '1.0.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
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 'InterMineR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:5: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:8: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:26: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:29: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:32: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:35: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:38: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:41: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:44: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:47: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:56: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:59: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:66: missing file link 'GRanges'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGeneAnswers.Rd:8: missing file link 'GeneAnswers'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:5: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:8: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:43: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:46: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:52: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:54: missing file link 'SummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:58: missing file link 'RangedSummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:61: missing file link 'SummarizedExperiment'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:69: missing file link 'RangedSummarizedExperiment'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/InterMineR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
** 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
convertToGeneAnswers: no visible binding for global variable
  'geneExpProfile'
convertToRangedSummarizedExperiment: no visible global function
  definition for 'reshape'
doEnrichment: no visible global function definition for 'URLencode'
listDatasets: no visible binding for global variable 'child_name'
runQuery,ANY-InterMineR: no visible global function definition for
  'URLencode'
runQuery,ANY-list: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode child_name geneExpProfile reshape
Consider adding
  importFrom("stats", "reshape")
  importFrom("utils", "URLencode")
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 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
convertToGeneAnswers                11.73   0.08   20.51
simplifyResult                       8.19   0.12    9.33
doEnrichment                         5.92   0.10   35.47
convertToRangedSummarizedExperiment  3.58   0.01    6.81
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
convertToGeneAnswers                22.66   0.12   30.59
simplifyResult                       9.13   0.05   10.14
doEnrichment                         6.24   0.13   35.80
convertToRangedSummarizedExperiment  5.44   0.03    8.82
* 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-3.6-bioc/meat/InterMineR.Rcheck/00check.log'
for details.

Installation output

InterMineR.Rcheck/00install.out


install for i386

* installing *source* package 'InterMineR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'InterMineR'
    finding HTML links ... done
    InterMineR-class                        html  
    InterMineR-methods                      html  
    InterMineR-package                      html  
    PL_DiabetesGenes                        html  
    PL_FlyTF_site_specific_TFs              html  
    convertToGRanges                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:5: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:8: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:26: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:29: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:32: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:35: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:38: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:41: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:44: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:47: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:56: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:59: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGRanges.Rd:66: missing file link 'GRanges'
    convertToGeneAnswers                    html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToGeneAnswers.Rd:8: missing file link 'GeneAnswers'
    convertToRangedSummarizedExperiment     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:5: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:8: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:43: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:46: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:52: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:54: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:58: missing file link 'RangedSummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:61: missing file link 'SummarizedExperiment'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpSmDrIl/R.INSTALL2a404f0f27/InterMineR/man/convertToRangedSummarizedExperiment.Rd:69: missing file link 'RangedSummarizedExperiment'
    doEnrichment                            html  
    getDatasets                             html  
    getGeneIds                              html  
    getModel                                html  
    getRelease                              html  
    getTemplateQuery                        html  
    getTemplates                            html  
    getVersion                              html  
    getWidgets                              html  
    initInterMine                           html  
    listDatasets                            html  
    listMines                               html  
    newQuery                                html  
    runQuery                                html  
    setConstraints                          html  
    setQuery                                html  
    simplifyResult                          html  
    summary                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'InterMineR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InterMineR' as InterMineR_1.0.0.zip
* DONE (InterMineR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

InterMineR.Rcheck/examples_i386/InterMineR-Ex.timings

nameusersystemelapsed
InterMineR-methods0.250.030.80
PL_DiabetesGenes000
PL_FlyTF_site_specific_TFs0.000.020.02
convertToGRanges0.810.031.22
convertToGeneAnswers11.73 0.0820.51
convertToRangedSummarizedExperiment3.580.016.81
doEnrichment 5.92 0.1035.47
getDatasets0.080.000.78
getGeneIds0.450.002.76
getModel1.200.032.00
getRelease0.00.00.3
getTemplateQuery0.020.000.31
getTemplates0.060.000.35
getVersion0.030.000.31
getWidgets0.020.000.61
initInterMine0.00.00.2
listDatasets2.030.033.41
listMines0.020.000.20
newQuery000
runQuery3.320.004.33
setConstraints0.070.000.58
setQuery0.040.000.53
simplifyResult8.190.129.33
summary0.020.000.29

InterMineR.Rcheck/examples_x64/InterMineR-Ex.timings

nameusersystemelapsed
InterMineR-methods0.360.050.89
PL_DiabetesGenes000
PL_FlyTF_site_specific_TFs0.020.000.02
convertToGRanges1.060.001.47
convertToGeneAnswers22.66 0.1230.59
convertToRangedSummarizedExperiment5.440.038.82
doEnrichment 6.24 0.1335.80
getDatasets0.090.000.78
getGeneIds0.620.012.94
getModel1.020.052.88
getRelease0.030.000.31
getTemplateQuery0.030.000.33
getTemplates0.030.000.32
getVersion0.040.000.32
getWidgets0.030.010.64
initInterMine0.010.000.22
listDatasets2.230.023.94
listMines0.010.000.21
newQuery000
runQuery3.410.004.45
setConstraints0.020.000.53
setQuery0.040.000.55
simplifyResult 9.13 0.0510.14
summary0.00.00.3