BioC 3.2: CHECK report for meshr on oaxaca

Package: meshr

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings meshr_1.6.2.tar.gz

StartedAt: 2016-04-23 01:53:07 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:02:35 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 568.3 seconds

RetCode: 0

Status:  OK

CheckDir: meshr.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings meshr_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/meshr.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘meshr/DESCRIPTION’ ... OK
* this is package ‘meshr’ version ‘1.6.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘meshr’ can be installed ... [34s/36s] OK
* checking installed package size ... NOTE
  installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    3.5Mb
* 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
* 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 loading without being on the library search path ... 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 binding for global variable ‘PMCID’
save.pdf,MeSHHyperGResult : <anonymous>: no visible binding for global
  variable ‘PMCID’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘MeSH.tex’, ‘fig1.png’, ‘fig2.png’, ‘fig3.png’, ‘fig4.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... [163s/225s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
meshHyperGTest 126.616 13.976 202.961
PMCID            4.926  0.135   5.099
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  ‘RSQLite’ ‘org.MeSH.Aca.db’ ‘org.MeSH.Atu.K84.db’
  ‘org.MeSH.Bsu.168.db’ ‘org.MeSH.Hsa.db’ ‘org.MeSH.Syn.db’
* 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: 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/meshr.Rcheck/00check.log’
for details.

* installing *source* package ‘meshr’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (meshr)

name	user	system	elapsed
PMCID	4.926	0.135	5.099
geneid.cummeRbund	0.016	0.003	0.050
meshHyperGTest	126.616	13.976	202.961
meshr-package	0.002	0.000	0.002
sig.geneid.cummeRbund	0.016	0.002	0.019