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CHECK report for AGDEX on tokay1

This page was generated on 2020-08-09 12:00:25 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AGDEX PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 36/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AGDEX 1.37.0
Cuilan lani Gao
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/AGDEX
Branch: master
Last Commit: b3b3d17
Last Changed Date: 2020-04-27 14:27:03 -0400 (Mon, 27 Apr 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 [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AGDEX
Version: 1.37.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AGDEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AGDEX_1.37.0.tar.gz
StartedAt: 2020-08-09 00:23:16 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 00:24:58 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 102.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: AGDEX.Rcheck
Warnings: 1

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:AGDEX.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AGDEX_1.37.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AGDEX.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AGDEX/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AGDEX' version '1.37.0'
* 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 'AGDEX' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/agdex.Rd:91: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/agdex.Rd:93: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/gset.data.Rd:24: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/human.data.Rd:35: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/make.dex.set.object.Rd:37: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/make.dex.set.object.Rd:39: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/mouse.data.Rd:35: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AGDEX.Rcheck/00install.out' for details.
* 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.
Non-standard license specification:
  GPL Version 2 or later
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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
Packages in Depends field not imported from:
  'Biobase' 'GSEABase'
  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
agdex: no visible global function definition for 'exprs'
agdex: no visible global function definition for 'qnorm'
agdex: no visible global function definition for 'pnorm'
agdex: no visible global function definition for 'sampleNames'
agdex: no visible global function definition for 'pData'
agdex.scatterplot: no visible global function definition for 'points'
agdex.scatterplot: no visible global function definition for 'lines'
agdex.scatterplot: no visible global function definition for 'prcomp'
agdex.scatterplot: no visible global function definition for 'abline'
gsc.to.index.list: no visible global function definition for 'geneIds'
prep.dex.set: no visible global function definition for 'exprs'
prep.dex.set: no visible global function definition for 'pData'
read.agdex.gset.details: no visible global function definition for
  'read.table'
read.agdex.gset.list: no visible global function definition for
  'read.table'
read.agdex.result: no visible global function definition for
  'read.table'
read.enrich.gset.list: no visible global function definition for
  'read.table'
read.gset.collection: no visible global function definition for
  'read.table'
read.gset.collection: no visible global function definition for
  'GeneSet'
read.gset.collection: no visible global function definition for
  'geneIds<-'
read.gset.collection: no visible global function definition for
  'GeneSetCollection'
write.agdex.gset.details: no visible global function definition for
  'write.table'
write.agdex.result: no visible global function definition for
  'write.table'
write.gset.list.result: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData
  pnorm points prcomp qnorm read.table sampleNames write.table
Consider adding
  importFrom("graphics", "abline", "lines", "points")
  importFrom("stats", "pnorm", "prcomp", "qnorm")
  importFrom("utils", "read.table", "write.table")
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
** running examples for arch 'x64' ... 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/AGDEX.Rcheck/00check.log'
for details.



Installation output

AGDEX.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/AGDEX_1.37.0.tar.gz && rm -rf AGDEX.buildbin-libdir && mkdir AGDEX.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AGDEX.buildbin-libdir AGDEX_1.37.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AGDEX_1.37.0.zip && rm AGDEX_1.37.0.tar.gz AGDEX_1.37.0.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  330k  100  330k    0     0  6239k      0 --:--:-- --:--:-- --:--:-- 6742k

install for i386

* installing *source* package 'AGDEX' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AGDEX'
    finding HTML links ... done
    AGDEX-package                           html  
    agdex                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/agdex.Rd:91: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/agdex.Rd:93: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
    agdex.res                               html  
    agdex.scatterplot                       html  
    get.gset.result.details                 html  
    gset.data                               html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/gset.data.Rd:24: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
    human.data                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/human.data.Rd:35: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    make.dex.set.object                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/make.dex.set.object.Rd:37: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/make.dex.set.object.Rd:39: file link 'GeneSetCollection' in package 'GSEABase' does not exist and so has been treated as a topic
    map.data                                html  
    mouse.data                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp8QKBVU/R.INSTALL1c5062fb36ef/AGDEX/man/mouse.data.Rd:35: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    read.agdex.gset.details                 html  
    read.agdex.result                       html  
    write.agdex.gset.details                html  
    write.agdex.result                      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 'AGDEX' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AGDEX' as AGDEX_1.37.0.zip
* DONE (AGDEX)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AGDEX' successfully unpacked and MD5 sums checked

Tests output


Example timings

AGDEX.Rcheck/examples_i386/AGDEX-Ex.timings

nameusersystemelapsed
agdex0.990.051.03
agdex.scatterplot0.050.000.05
get.gset.result.details0.030.000.03
gset.data000
human.data0.020.000.01
make.dex.set.object0.030.030.06
map.data000
mouse.data0.030.000.04
read.agdex.gset.details000
read.agdex.result000
write.agdex.gset.details0.030.000.03
write.agdex.result0.020.000.01

AGDEX.Rcheck/examples_x64/AGDEX-Ex.timings

nameusersystemelapsed
agdex0.890.060.95
agdex.scatterplot0.060.000.07
get.gset.result.details0.050.020.07
gset.data000
human.data0.020.010.03
make.dex.set.object0.030.030.06
map.data000
mouse.data0.010.020.03
read.agdex.gset.details000
read.agdex.result0.000.010.02
write.agdex.gset.details0.050.000.04
write.agdex.result0.020.000.02