Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-07-30 15:05:47 -0400 (Fri, 30 Jul 2021).

CHECK results for Category on tokay2

To the developers/maintainers of the Category package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Category.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 245/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Category 2.58.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/Category
Branch: RELEASE_3_13
Last Commit: 5a966e0
Last Changed Date: 2021-05-19 11:35:55 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Category
Version: 2.58.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Category.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Category_2.58.0.tar.gz
StartedAt: 2021-07-29 20:57:24 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 21:05:04 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 460.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Category.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Category.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Category_2.58.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Category.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Category/DESCRIPTION' ... OK
* this is package 'Category' version '2.58.0'
* 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 'Category' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package 'KEGG.db' in Rd xrefs
* 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
HyperGResult-accessors 1.17   0.21    5.67
** running examples for arch 'x64' ... OK
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/Category.Rcheck/00check.log'
for details.



Installation output

Category.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Category_2.58.0.tar.gz && rm -rf Category.buildbin-libdir && mkdir Category.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Category.buildbin-libdir Category_2.58.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Category_2.58.0.zip && rm Category_2.58.0.tar.gz Category_2.58.0.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
  1  163k    1  2487    0     0  45846      0  0:00:03 --:--:--  0:00:03 46055
100  163k  100  163k    0     0  1120k      0 --:--:-- --:--:-- --:--:-- 1122k

install for i386

* installing *source* package 'Category' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Category'
    finding HTML links ... done
    Category-defunct                        html  
    ChrBandTree-class                       html  
    ChrMapHyperGParams-class                html  
REDIRECT:topic	 conditional<-,ChrMapHyperGParams,logical-method -> ChrMapHyperGParams-class.html [ FAIL ]
    ChrMapHyperGResult-class                html  
    ChrMapLinearMParams-class               html  
    ChrMapLinearMResult-class               html  
    DatPkg-class                            html  
    GOHyperGParams-class                    html  
REDIRECT:topic	 conditional<-,GOHyperGParams,logical-method -> GOHyperGParams-class.html [ FAIL ]
REDIRECT:topic	 ontology<-,GOHyperGParams,character-method -> GOHyperGParams-class.html [ FAIL ]
    GSEAGOHyperGParams                      html  
    HyperGParams-class                      html  
REDIRECT:topic	 conditional<- -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 geneIds<- -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 ontology<- -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 pvalueCutoff<- -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 testDirection<- -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 geneIds<-,HyperGParams,logical-method -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 geneIds<-,HyperGParams,ANY-method -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 annotation<-,HyperGParams,character-method -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 pvalueCutoff<-,HyperGParams-method -> HyperGParams-class.html [ FAIL ]
REDIRECT:topic	 testDirection<-,HyperGParams-method -> HyperGParams-class.html [ FAIL ]
    HyperGResult-accessors                  html  
    HyperGResult-class                      html  
    HyperGResultBase-class                  html  
    KEGGHyperGParams-class                  html  
    LinearMParams-class                     html  
REDIRECT:topic	 annotation<-,LinearMParams,character-method -> LinearMParams-class.html [ FAIL ]
REDIRECT:topic	 conditional<-,LinearMParams,logical-method -> LinearMParams-class.html [ FAIL ]
REDIRECT:topic	 geneIds<-,LinearMParams,ANY-method -> LinearMParams-class.html [ FAIL ]
REDIRECT:topic	 pvalueCutoff<-,LinearMParams-method -> LinearMParams-class.html [ FAIL ]
REDIRECT:topic	 testDirection<-,LinearMParams-method -> LinearMParams-class.html [ FAIL ]
    LinearMResult-class                     html  
    LinearMResultBase-class                 html  
    MAPAmat                                 html  
    NewChrBandTree                          html  
    OBOHyperGParams-class                   html  
REDIRECT:topic	 conditional<-,OBOHyperGParams,logical-method -> OBOHyperGParams-class.html [ FAIL ]
    applyByCategory                         html  
    cateGOryMatrix                          html  
    categoryToEntrezBuilder                 html  
    cb_contingency                          html  
    cb_parse_band_Hs                        html  
    cb_parse_band_Mm                        html  
    cb_test                                 html  
    effectSize                              html  
    exampleLevels                           html  
    findAMstats                             html  
    getPathNames                            html  
    gseattperm                              html  
    hyperGTest                              html  
    hyperg                                  html  
    linearMTest                             html  
    local_test_factory                      html  
    makeChrBandGraph                        html  
    makeEBcontr                             html  
    makeValidParams                         html  
    probes2MAP                              html  
    probes2Path                             html  
    tree_visitor                            html  
    ttperm                                  html  
    universeBuilder                         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 'Category' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Category' as Category_2.58.0.zip
* DONE (Category)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Category' successfully unpacked and MD5 sums checked

Tests output

Category.Rcheck/tests_i386/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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("Category") || stop("unable to load Category")
Loading required package: Category
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

Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

[1] TRUE
> BiocGenerics:::testPackage("Category", "UnitTests", ".*_test\\.R$")
Loading required package: org.Hs.eg.db



'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: graph


Attaching package: 'GOstats'

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

    makeGOGraph



RUNIT TEST PROTOCOL -- Thu Jul 29 21:03:50 2021 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Category RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In makeValidParams(.Object) : removing duplicate IDs in geneIds
2: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
3: In makeValidParams(.Object) : removing geneIds not in universeGeneIds
4: In makeValidParams(.Object) : removing duplicate IDs in geneIds
5: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
6: In makeValidParams(.Object) : removing geneIds not in universeGeneIds
7: In makeValidParams(.Object) :
  converting geneIds from list to atomic vector via unlist
8: In makeValidParams(.Object) :
  converting univ from list to atomic vector via unlist
9: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> proc.time()
   user  system elapsed 
  56.75   25.29  154.81 

Category.Rcheck/tests_x64/runTests.Rout


R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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("Category") || stop("unable to load Category")
Loading required package: Category
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

Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

[1] TRUE
> BiocGenerics:::testPackage("Category", "UnitTests", ".*_test\\.R$")
Loading required package: org.Hs.eg.db



'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
Loading required package: graph


Attaching package: 'GOstats'

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

    makeGOGraph



RUNIT TEST PROTOCOL -- Thu Jul 29 21:04:55 2021 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Category RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In makeValidParams(.Object) : removing duplicate IDs in geneIds
2: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
3: In makeValidParams(.Object) : removing geneIds not in universeGeneIds
4: In makeValidParams(.Object) : removing duplicate IDs in geneIds
5: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
6: In makeValidParams(.Object) : removing geneIds not in universeGeneIds
7: In makeValidParams(.Object) :
  converting geneIds from list to atomic vector via unlist
8: In makeValidParams(.Object) :
  converting univ from list to atomic vector via unlist
9: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> proc.time()
   user  system elapsed 
  46.85   18.37   65.26 

Example timings

Category.Rcheck/examples_i386/Category-Ex.timings

nameusersystemelapsed
ChrBandTree-class3.080.303.37
ChrMapHyperGParams-class000
ChrMapHyperGResult-class000
ChrMapLinearMParams-class000
ChrMapLinearMResult-class000
DatPkg-class0.030.000.04
HyperGResult-accessors1.170.215.67
LinearMResult-class000
MAPAmat3.000.133.13
applyByCategory0.020.000.01
cateGOryMatrix0.370.030.41
cb_parse_band_Hs000
cb_parse_band_Mm000
findAMstats0.020.000.02
getPathNames0.060.001.73
gseattperm1.940.062.00
hyperg0.500.020.52
makeChrBandGraph1.790.001.79
makeEBcontr0.130.000.13
probes2MAP0.110.000.11
probes2Path0.030.000.03
ttperm0.010.000.01

Category.Rcheck/examples_x64/Category-Ex.timings

nameusersystemelapsed
ChrBandTree-class4.470.074.53
ChrMapHyperGParams-class000
ChrMapHyperGResult-class000
ChrMapLinearMParams-class000
ChrMapLinearMResult-class000
DatPkg-class0.030.000.03
HyperGResult-accessors0.990.031.01
LinearMResult-class000
MAPAmat4.280.034.31
applyByCategory0.010.000.02
cateGOryMatrix0.380.020.39
cb_parse_band_Hs000
cb_parse_band_Mm000
findAMstats000
getPathNames0.050.001.32
gseattperm1.590.091.68
hyperg0.690.000.69
makeChrBandGraph202
makeEBcontr0.140.000.14
probes2MAP0.160.000.15
probes2Path0.080.000.08
ttperm0.030.000.03