Package: meshes

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshes.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings meshes_1.8.0.tar.gz

StartedAt: 2019-03-20 04:42:33 -0400 (Wed, 20 Mar 2019)

EndedAt: 2019-03-20 04:46:21 -0400 (Wed, 20 Mar 2019)

EllapsedTime: 228.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: meshes.Rcheck

Warnings: 5

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshes.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings meshes_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/meshes.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 = lib.
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
meshdata 8.11   0.78   33.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
meshdata 7.39   0.75    8.14
* 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: 5 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/meshes.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/meshes_1.8.0.tar.gz && rm -rf meshes.buildbin-libdir && mkdir meshes.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=meshes.buildbin-libdir meshes_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL meshes_1.8.0.zip && rm meshes_1.8.0.tar.gz meshes_1.8.0.zip
###
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100  882k  100  882k    0     0  16.7M      0 --:--:-- --:--:-- --:--:-- 17.9M

install for i386

* installing *source* package 'meshes' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'meshes'
    finding HTML links ... done
    enrichMeSH                              html  
    geneSim                                 html  
    gseMeSH                                 html  
    meshSim                                 html  
    mesh_term_table                         html  
    meshdata                                html  
    reexports                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'meshes' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'meshes' as meshes_1.8.0.zip
* DONE (meshes)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'meshes' successfully unpacked and MD5 sums checked
In R CMD INSTALL