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CHECK report for meshes on merida1

This page was generated on 2019-04-16 12:00:05 -0400 (Tue, 16 Apr 2019).

Package 911/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
meshes 1.8.0
Guangchuang Yu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/meshes
Branch: RELEASE_3_8
Last Commit: c84c001
Last Changed Date: 2018-10-30 11:42:03 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: meshes
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:meshes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings meshes_1.8.0.tar.gz
StartedAt: 2019-04-16 01:06:07 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:08:37 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 150.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: meshes.Rcheck
Warnings: 3

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:meshes.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings meshes_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/meshes.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘meshes/DESCRIPTION’ ... OK
* this is package ‘meshes’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ‘meshes’ 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 ... WARNING
Found the following file with non-ASCII characters:
  zzz.R
Portable packages must use only ASCII characters in their R code,
except perhaps in comments.
Use \uxxxx escapes for other characters.
* 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 ...
Error: package or namespace load failed for ‘meshes’:
 .onLoad failed in loadNamespace() for 'meshes', details:
  call: packageDescription(pkgname, fields = "Version")
  error: could not find function "packageDescription"
Execution halted

It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package.  All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... WARNING
Error: package or namespace load failed for ‘meshes’:
 .onLoad failed in loadNamespace() for 'meshes', details:
  call: packageDescription(pkgname, fields = "Version")
  error: could not find function "packageDescription"
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Error: .onLoad failed in loadNamespace() for 'meshes', details:
  call: packageDescription(pkgname, fields = "Version")
  error: could not find function "packageDescription"
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Error: package or namespace load failed for ‘meshes’:
 .onLoad failed in loadNamespace() for 'meshes', details:
  call: packageDescription(pkgname, fields = "Version")
  error: could not find function "packageDescription"
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)
   }, 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(package, lib.loc = 
Execution halted
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘meshes/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste0(msg, citation))

See section ‘Good practice’ in '?.onAttach'.

Error: .onLoad failed in loadNamespace() for 'meshes', details:
  call: packageDescription(pkgname, fields = "Version")
  error: could not find function "packageDescription"
Execution halted
* 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 ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
meshdata 9.613  0.895  10.882
* 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: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/meshes.Rcheck/00check.log’
for details.



Installation output

meshes.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL meshes
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘meshes’ ...
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (meshes)

Tests output


Example timings

meshes.Rcheck/meshes-Ex.timings

nameusersystemelapsed
enrichMeSH000
geneSim3.2120.2313.477
gseMeSH000
meshSim0.5740.0540.638
meshdata 9.613 0.89510.882