meshr 1.2.7
Koki Tsuyuzaki
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/meshr | | Last Changed Rev: 101574 / Revision: 102249 | | Last Changed Date: 2015-03-29 23:36:21 -0700 (Sun, 29 Mar 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | TIMEOUT | skipped | skipped |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | TIMEOUT | skipped | skipped |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch meshr_1.2.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/meshr.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘meshr/DESCRIPTION’ ... OK
* this is package ‘meshr’ version ‘1.2.7’
* 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’ ‘org.MeSH.Hsa.db’
‘org.MeSH.Aca.db’ ‘org.MeSH.Atu.K84.db’ ‘org.MeSH.Bsu.168.db’
‘org.MeSH.Syn.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 ... [64s/68s] 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 ... 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 ... 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 look like leftovers/mistakes:
‘MeSH.bbl’
Please remove them from your package.
The following files should probably not be installed:
‘fig1.png’, ‘fig2.png’, ‘fig3.png’, ‘fig4.png’, ‘MeSH.tex’
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’ ... NOTE
The following files look like leftovers/mistakes:
‘MeSH.bbl’
Please remove them from your package.
* checking examples ... [10m/11m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
meshHyperGTest 564.464 18.956 590.042
PMCID 11.573 0.335 11.909
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘RSQLite’
* 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
NOTE: There were 7 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/meshr.Rcheck/00check.log’
for details.