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CHECK report for affycoretools on malbec1

This page was generated on 2021-01-25 11:48:00 -0500 (Mon, 25 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE affycoretools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 28/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycoretools 1.62.0
James W. MacDonald
Snapshot Date: 2021-01-24 14:40:16 -0500 (Sun, 24 Jan 2021)
URL: https://git.bioconductor.org/packages/affycoretools
Branch: RELEASE_3_12
Last Commit: c9779e4
Last Changed Date: 2020-10-27 10:27:23 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 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  ERROR  OK 

Summary

Package: affycoretools
Version: 1.62.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:affycoretools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings affycoretools_1.62.0.tar.gz
StartedAt: 2021-01-24 23:19:48 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 23:27:40 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 472.2 seconds
RetCode: 0
Status:  OK 
CheckDir: affycoretools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:affycoretools.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings affycoretools_1.62.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/affycoretools.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affycoretools/DESCRIPTION’ ... OK
* this is package ‘affycoretools’ version ‘1.62.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘affycoretools’ 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 ... NOTE
Error: package or namespace load failed for ‘affycoretools’:
 .onLoad failed in loadNamespace() for 'biomaRt', details:
  call: httr::set_config(new_config, override = FALSE)
  error: object 'new_config' not found
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(pack
Execution halted
* 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 ... 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/affycoretools.Rcheck/00check.log’
for details.



Installation output

affycoretools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL affycoretools
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘affycoretools’ ...
** using staged installation
** R
** 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 (affycoretools)

Tests output


Example timings

affycoretools.Rcheck/affycoretools-Ex.timings

nameusersystemelapsed
annotateEset000
doGlimma000
entrezLinks000
makeVenn0.0000.0000.001
plotDeg3.7920.1243.921
plotPCA0.0640.0040.069
vennCounts20.0760.0000.077
vennPage000