Bioconductor Package Maintainer
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/GOstats |
| Branch: RELEASE_3_11 |
| Last Commit: bc985b6 |
| Last Changed Date: 2020-04-27 14:09:54 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:45 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE GOstats PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 758/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GOstats 2.54.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: GOstats |
| Version: 2.54.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GOstats_2.54.0.tar.gz |
| StartedAt: 2020-10-17 04:37:55 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:45:21 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 446.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GOstats.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings GOstats_2.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GOstats.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'GOstats/DESCRIPTION' ... OK * this is package 'GOstats' version '2.54.0' * 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 'GOstats' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp2Hsu8R/R.INSTALL203c21ca20cc/GOstats/man/hyperGTest.Rd:47: file link 'geneGoHyperGeoTest' in package 'Category' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp2Hsu8R/R.INSTALL203c21ca20cc/GOstats/man/hyperGTest.Rd:48: file link 'geneKeggHyperGeoTest' in package 'Category' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GOstats.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 ... 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 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 '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 WARNING See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/GOstats.Rcheck/00check.log' for details.
GOstats.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/GOstats_2.54.0.tar.gz && rm -rf GOstats.buildbin-libdir && mkdir GOstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOstats.buildbin-libdir GOstats_2.54.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL GOstats_2.54.0.zip && rm GOstats_2.54.0.tar.gz GOstats_2.54.0.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 1571k 100 1571k 0 0 15.7M 0 --:--:-- --:--:-- --:--:-- 16.8M
install for i386
* installing *source* package 'GOstats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GOstats'
finding HTML links ... done
GOHyperGResult-class html
GOstats-defunct html
GOstats-package html
Ndists html
OBOHyperGResult-class html
compCorrGraph html
compGdist html
hyperGTest html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp2Hsu8R/R.INSTALL203c21ca20cc/GOstats/man/hyperGTest.Rd:47: file link 'geneGoHyperGeoTest' in package 'Category' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp2Hsu8R/R.INSTALL203c21ca20cc/GOstats/man/hyperGTest.Rd:48: file link 'geneKeggHyperGeoTest' in package 'Category' does not exist and so has been treated as a topic
idx2dimnames html
makeGOGraph html
notConn html
oneGOGraph html
probeSetSummary html
shortestPath html
simLL html
termGraphs html
triadCensus 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 'GOstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOstats' as GOstats_2.54.0.zip
* DONE (GOstats)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'GOstats' successfully unpacked and MD5 sums checked
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GOstats.Rcheck/tests_i386/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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("GOstats") || stop("unable to load GOstats")
Loading required package: GOstats
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
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
Loading required package: graph
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
[1] TRUE
> BiocGenerics:::testPackage("GOstats", "UnitTests", ".*_test\\.R$")
Loading required package: org.Hs.eg.db
RUNIT TEST PROTOCOL -- Sat Oct 17 04:43:02 2020
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
GOstats RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
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
73.79 40.00 113.82
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GOstats.Rcheck/tests_x64/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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("GOstats") || stop("unable to load GOstats")
Loading required package: GOstats
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
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
Loading required package: graph
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
[1] TRUE
> BiocGenerics:::testPackage("GOstats", "UnitTests", ".*_test\\.R$")
Loading required package: org.Hs.eg.db
RUNIT TEST PROTOCOL -- Sat Oct 17 04:44:51 2020
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
GOstats RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
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
66.56 37.70 108.56
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GOstats.Rcheck/examples_i386/GOstats-Ex.timings
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GOstats.Rcheck/examples_x64/GOstats-Ex.timings
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