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This page was generated on 2021-08-05 12:05:56 -0400 (Thu, 05 Aug 2021).

CHECK results for GOstats on nebbiolo2

To the developers/maintainers of the GOstats package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOstats.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 781/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOstats 2.59.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-08-04 14:50:10 -0400 (Wed, 04 Aug 2021)
URL: https://git.bioconductor.org/packages/GOstats
Branch: master
Last Commit: b110124
Last Changed Date: 2021-05-19 11:34:28 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GOstats
Version: 2.59.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GOstats.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GOstats_2.59.0.tar.gz
StartedAt: 2021-08-04 19:55:00 -0400 (Wed, 04 Aug 2021)
EndedAt: 2021-08-04 19:58:44 -0400 (Wed, 04 Aug 2021)
EllapsedTime: 223.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GOstats.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GOstats.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GOstats_2.59.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GOstats.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOstats/DESCRIPTION’ ... OK
* this is package ‘GOstats’ version ‘2.59.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GOstats’ 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
* 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 ... ERROR
Running examples in ‘GOstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: probeSetSummary
> ### Title: Summarize Probe Sets Associated with a hyperGTest Result
> ### Aliases: probeSetSummary
> ### Keywords: manip htest
> 
> ### ** Examples
> 
>   ## Fake up some data
>   library("hgu95av2.db")
Loading required package: org.Hs.eg.db
>   library("annotate")
Loading required package: XML

Attaching package: ‘XML’

The following object is masked from ‘package:graph’:

    addNode

>   prbs <- ls(hgu95av2GO)[1:300]
>   ## Only those with GO ids
>   hasGO <- sapply(mget(prbs, hgu95av2GO), function(ids)
+   if(!is.na(ids) && length(ids) > 1) TRUE else FALSE)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
package:annotate
 --- call from context --- 
FUN(X[[i]], ...)
 --- call from argument --- 
!is.na(ids) && length(ids) > 1
 --- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: lapply(X = X, FUN = FUN, ...)
where 3: sapply(mget(prbs, hgu95av2GO), function(ids) if (!is.na(ids) && 
    length(ids) > 1) TRUE else FALSE)
where 4: sapply(mget(prbs, hgu95av2GO), function(ids) if (!is.na(ids) && 
    length(ids) > 1) TRUE else FALSE)

 --- value of length: 103 type: logical ---
GO:0000165 GO:0000165 GO:0000186 GO:0000187 GO:0001934 GO:0006361 GO:0006468 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0006915 GO:0006975 GO:0007049 GO:0007166 GO:0007411 GO:0007568 GO:0008543 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0009636 GO:0010628 GO:0010759 GO:0014066 GO:0016032 GO:0016310 GO:0018105 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0019233 GO:0019369 GO:0030168 GO:0030278 GO:0030509 GO:0030641 GO:0030878 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0031281 GO:0031663 GO:0032212 GO:0032872 GO:0033129 GO:0034198 GO:0034614 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0035066 GO:0035556 GO:0038083 GO:0038095 GO:0038096 GO:0042473 GO:0043330 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0045727 GO:0045944 GO:0046697 GO:0048538 GO:0051090 GO:0051216 GO:0051403 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0051493 GO:0051973 GO:0060020 GO:0060324 GO:0060425 GO:0060440 GO:0061308 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0065003 GO:0070371 GO:0070374 GO:0070498 GO:0070849 GO:0071260 GO:0071276 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0071356 GO:0072584 GO:0090170 GO:0120041 GO:1900034 GO:1903351 GO:1904355 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:1904417 GO:2000641 GO:2000657 GO:0005634 GO:0005634 GO:0005635 GO:0005654 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0005737 GO:0005737 GO:0005739 GO:0005769 GO:0005770 GO:0005794 GO:0005829 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0005856 GO:0005886 GO:0005901 GO:0005901 GO:0005925 GO:0031143 GO:0032991 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0001784 GO:0004674 GO:0004674 GO:0004707 GO:0004707 GO:0004707 GO:0004708 
      TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
GO:0005515 GO:0005524 GO:0019902 GO:0042802 GO:0097110 
      TRUE       TRUE       TRUE       TRUE       TRUE 
 --- function from context --- 
function (ids) 
if (!is.na(ids) && length(ids) > 1) TRUE else FALSE
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Error in !is.na(ids) && length(ids) > 1 : 
  'length(x) = 103 > 1' in coercion to 'logical(1)'
Calls: sapply -> sapply -> lapply -> FUN
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 ERROR
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/GOstats.Rcheck/00check.log’
for details.


Installation output

GOstats.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GOstats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘GOstats’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (GOstats)

Tests output

GOstats.Rcheck/tests/runTests.Rout


R version 4.1.0 beta (2021-05-03 r80259) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

Attaching package: 'BiocGenerics'

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

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 objects are masked from 'package:base':

    I, expand.grid, unname

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 -- Wed Aug  4 19:58:41 2021 
*********************************************** 
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) :
  converting univ from list to atomic vector via unlist
3: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> proc.time()
   user  system elapsed 
 67.028  21.139  94.680 

Example timings

GOstats.Rcheck/GOstats-Ex.timings

nameusersystemelapsed
Ndists0.0300.0040.034
compCorrGraph0.4380.0160.454
compGdist0.7060.0040.710
idx2dimnames0.0180.0000.018
makeGOGraph0.8280.0440.872
notConn0.0380.0040.041
oneGOGraph0.2560.0000.257