Bioconductor Package Maintainer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Category |
| Branch: RELEASE_3_10 |
| Last Commit: 71e3a7a |
| Last Changed Date: 2019-11-08 12:20:13 -0400 (Fri, 08 Nov 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:17:20 -0400 (Wed, 15 Apr 2020).
| Package 229/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Category 2.52.1 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Category |
| Version: 2.52.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Category.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Category_2.52.1.tar.gz |
| StartedAt: 2020-04-15 01:50:11 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:56:28 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 377.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Category.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Category.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Category_2.52.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Category.Rcheck' * using R version 3.6.3 (2020-02-29) * 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 '2.52.1' * 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 ... 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 ... 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 ** 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: OK
Category.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Category_2.52.1.tar.gz && rm -rf Category.buildbin-libdir && mkdir Category.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Category.buildbin-libdir Category_2.52.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Category_2.52.1.zip && rm Category_2.52.1.tar.gz Category_2.52.1.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 162k 100 162k 0 0 4435k 0 --:--:-- --:--:-- --:--:-- 4925k
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
ChrMapHyperGResult-class html
ChrMapLinearMParams-class html
ChrMapLinearMResult-class html
DatPkg-class html
GOHyperGParams-class html
GSEAGOHyperGParams html
HyperGParams-class html
HyperGResult-accessors html
HyperGResult-class html
HyperGResultBase-class html
KEGGHyperGParams-class html
LinearMParams-class html
LinearMResult-class html
LinearMResultBase-class html
MAPAmat html
NewChrBandTree html
OBOHyperGParams-class html
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_2.52.1.zip
* DONE (Category)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Category' successfully unpacked and MD5 sums checked
|
Category.Rcheck/tests_i386/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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("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, 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 object is masked from 'package:base':
expand.grid
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$")
Loading required package: org.Hs.eg.db
Error in x$.self$finalize() : attempt to apply non-function
In addition: 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
Error in (function (x) : attempt to apply non-function
'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 -- Wed Apr 15 01:54:59 2020
***********************************************
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) :
converting geneIds from list to atomic vector via unlist
2: In makeValidParams(.Object) : removing duplicate IDs in geneIds
3: In makeValidParams(.Object) :
converting univ from list to atomic vector via unlist
4: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
>
> proc.time()
user system elapsed
58.07 25.32 100.18
|
Category.Rcheck/tests_x64/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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("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, 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 object is masked from 'package:base':
expand.grid
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 -- Wed Apr 15 01:56:22 2020
***********************************************
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) : removing duplicate IDs in geneIds
9: In makeValidParams(.Object) :
converting univ from list to atomic vector via unlist
10: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
>
> proc.time()
user system elapsed
57.53 24.06 81.73
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Category.Rcheck/examples_i386/Category-Ex.timings
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Category.Rcheck/examples_x64/Category-Ex.timings
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