meshr 1.0.4
Koki Tsuyuzaki
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/meshr | | Last Changed Rev: 93894 / Revision: 95116 | | Last Changed Date: 2014-09-07 05:17:35 -0700 (Sun, 07 Sep 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf meshr.buildbin-libdir && mkdir meshr.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=meshr.buildbin-libdir meshr_1.0.4.tar.gz >meshr-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=meshr.buildbin-libdir --install="check:meshr-install.out" --force-multiarch --no-vignettes --timings meshr_1.0.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/meshr.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'meshr/DESCRIPTION' ... OK
* this is package 'meshr' version '1.0.4'
* 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'
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 ... 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 ... 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 ... OK
* 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(mesh.cat, 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'
* 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:
'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' ... [544s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
meshHyperGTest 68.45 4.51 526.19
** running examples for arch 'x64' ... [92s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
meshHyperGTest 66.63 1.36 67.98
* 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
NOTE: There were 4 notes.
See
'E:/biocbld/bbs-2.14-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_1.0.4.zip
* DONE (meshr)