Package: meshr

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings meshr_1.16.0.tar.gz

StartedAt: 2018-10-17 03:10:14 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 03:24:50 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 875.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: meshr.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:meshr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings meshr_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/meshr.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'meshr/DESCRIPTION' ... OK
* this is package 'meshr' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'fdrtool' 'Category' 'BiocGenerics' 'cummeRbund' 'org.Hs.eg.db'
  'MeSH.db' 'MeSH.AOR.db' 'MeSH.PCR.db' 'MeSHDbi' 'MeSH.Hsa.eg.db'
  'MeSH.Aca.eg.db' 'MeSH.Bsu.168.eg.db' 'MeSH.Syn.eg.db' 'S4Vectors'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'meshr' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Unexported object imported by a ':::' call: 'Category:::.doHyperGInternal'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.meshHyperGTestInternal: warning in switch(p@category, A = {: partial
  argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Anatomy": partial
  argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, B = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Organisms":
  partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, C = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Diseases":
  partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, D = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Chemicals and
  Drugs": partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, E = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Analytical,
  Diagnostic and Therapeutic Techniques and Equipment": partial
  argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, F = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Psychiatry and
  Psychology": partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, G = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Phenomena and
  Processes": partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, H = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Disciplines and
  Occupations": partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, I = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Anthropology,
  Education, Sociology and Social Phenomena": partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, J = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Technology and
  Food and Beverages": partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, K = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Humanities":
  partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, L = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Information
  Science": partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, M = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Persons": partial
  argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, N = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Health Care":
  partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, V = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Publication
  Type": partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }, Z = {: partial argument match of
  'E' to 'EXPR'
.meshHyperGTestInternal: warning in mesh.full.cat <- "Geographical
  Locations": partial argument match of 'E' to 'EXPR'
.meshHyperGTestInternal: warning in }): partial argument match of 'E'
  to 'EXPR'
.convert_PMID_PMCID: no visible global function definition for 'data'
.convert_PMID_PMCID: no visible binding for global variable 'PMCID'
.download_PMCPDF : <anonymous>: no visible global function definition
  for 'download.file'
.meshHyperGTestInternal: no visible global function definition for
  'p.adjust'
.sapply_pb: no visible global function definition for 'txtProgressBar'
.sapply_pb : wrapper: no visible global function definition for
  'setTxtProgressBar'
save.pdf,MeSHHyperGResult: no visible global function definition for
  'download.file'
save.pdf,MeSHHyperGResult: no visible global function definition for
  'read.delim'
save.pdf,MeSHHyperGResult : <anonymous>: no visible binding for global
  variable 'PMCID'
Undefined global functions or variables:
  PMCID data download.file p.adjust read.delim setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("stats", "p.adjust")
  importFrom("utils", "data", "download.file", "read.delim",
             "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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' ... ERROR
Running examples in 'meshr-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meshHyperGTest
> ### Title: Hypergeometric Tests for MeSH term association
> ### Aliases: meshHyperGTest meshHyperGTest,MeSHHyperGParams-method
> ### Keywords: models
> 
> ### ** Examples
> 
> data(geneid.cummeRbund)
> data(sig.geneid.cummeRbund)
> 
> meshParams <- new("MeSHHyperGParams", geneIds=sig.geneid.cummeRbund[,2], universeGeneIds=geneid.cummeRbund[,2], annotation="MeSH.Hsa.eg.db", category="Z", database="gene2pubmed", pvalueCutoff=0.05, pAdjust="none")
> 
> meshR <- meshHyperGTest(meshParams)
Error: memory exhausted (limit reached?)
Execution halted
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
meshHyperGTest 164.08  14.01  178.59
* 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, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/meshr.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/meshr_1.16.0.tar.gz && rm -rf meshr.buildbin-libdir && mkdir meshr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=meshr.buildbin-libdir meshr_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL meshr_1.16.0.zip && rm meshr_1.16.0.tar.gz meshr_1.16.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 6342k  100 6342k    0     0  55.0M      0 --:--:-- --:--:-- --:--:-- 57.8M

install for i386

* installing *source* package 'meshr' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'meshr'
    finding HTML links ... done
    MeSHHyperGParams-class                  html  
    MeSHHyperGResult-class                  html  
    PMCID                                   html  
    category                                html  
    database                                html  
    geneid.cummeRbund                       html  
    meshHyperGTest                          html  
    meshr-package                           html  
    sig.geneid.cummeRbund                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'meshr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'meshr' as meshr_1.16.0.zip
* DONE (meshr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'meshr' successfully unpacked and MD5 sums checked
In R CMD INSTALL