Package: meshes

Version: 1.8.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:meshes.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings meshes_1.8.0.tar.gz

StartedAt: 2019-04-16 01:13:59 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:16:19 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 140.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: meshes.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:meshes.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings meshes_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/meshes.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 9.836  0.204  10.206
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/meshes.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL meshes
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

name	user	system	elapsed
enrichMeSH	0	0	0
geneSim	3.744	0.056	3.822
gseMeSH	0	0	0
meshSim	0.628	0.024	0.655
meshdata	9.836	0.204	10.206