meshr 1.12.0
Koki Tsuyuzaki
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/meshr | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf meshr.buildbin-libdir meshr.Rcheck && mkdir meshr.buildbin-libdir meshr.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=meshr.buildbin-libdir meshr_1.12.0.tar.gz >meshr.Rcheck\00install.out 2>&1 && cp meshr.Rcheck\00install.out meshr-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=meshr.buildbin-libdir --install="check:meshr-install.out" --force-multiarch --no-vignettes --timings meshr_1.12.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/meshr.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.12.0'
* 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 8.3Mb
sub-directories of 1Mb or more:
data 4.5Mb
doc 3.4Mb
* 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
** checking loading without being on the library search path ... 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 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 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
meshHyperGTest 123.7 14.83 271.63
PMCID 5.6 0.24 5.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
meshHyperGTest 148.67 6.81 155.51
PMCID 5.78 0.11 5.89
* 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: 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/meshr.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'meshr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'meshr' as meshr_1.12.0.zip
* DONE (meshr)