pathview 1.16.5
Weijun Luo
| 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/pathview | | Last Changed Rev: 131566 / Revision: 131943 | | Last Changed Date: 2017-07-25 12:33:06 -0400 (Tue, 25 Jul 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf pathview.buildbin-libdir pathview.Rcheck && mkdir pathview.buildbin-libdir pathview.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathview.buildbin-libdir pathview_1.16.5.tar.gz >pathview.Rcheck\00install.out 2>&1 && cp pathview.Rcheck\00install.out pathview-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=pathview.buildbin-libdir --install="check:pathview-install.out" --force-multiarch --no-vignettes --timings pathview_1.16.5.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/pathview.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 'pathview/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathview' version '1.16.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'pathview' 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
* 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
Package in Depends field not imported from: 'org.Hs.eg.db'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'pathview/R/zzz.R':
.onLoad calls:
installed.packages()
packageStartupMessage(wordwrap(disclaimer, 80))
Package startup functions should not call 'installed.packages'.
See section 'Good practice' in '?.onAttach'.
col.key: no visible binding for global variable 'node.sizes'
cpd2kegg: no visible binding for global variable 'rn.list'
cpdidmap: no visible binding for global variable 'cpd.accs'
cpdkegg2name: no visible binding for global variable 'kegg.met'
cpdname2kegg: no visible binding for global variable 'cpd.names'
download.kegg: no visible global function definition for
'download.file'
geneannot.map: no visible binding for global variable 'bods'
geneannot.map: no visible global function definition for 'biocLite'
geneannot.map: no visible global function definition for 'columns'
geneannot.map: no visible global function definition for 'select'
kegg.species.code: no visible binding for global variable 'korg'
keggview.graph: no visible binding for global variable
'KEGGEdgeSubtype'
pathview: no visible binding for global variable 'bods'
pathview: no visible binding for global variable 'rn.list'
sim.mol.data: no visible binding for global variable 'bods'
sim.mol.data: no visible global function definition for 'biocLite'
sim.mol.data: no visible global function definition for 'keys'
sim.mol.data: no visible binding for global variable 'cpd.accs'
sim.mol.data: no visible binding for global variable 'rn.list'
sim.mol.data: no visible binding for global variable 'ko.ids'
subtypeDisplay,KEGGEdge: Error while checking: only works for closures
Undefined global functions or variables:
KEGGEdgeSubtype biocLite bods columns cpd.accs cpd.names
download.file kegg.met keys ko.ids korg node.sizes rn.list select
Consider adding
importFrom("utils", "download.file")
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' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pathview 12.72 2.37 15.66
sim.mol.data 1.33 0.08 10.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pathview 15.26 2.58 18.33
sim.mol.data 1.41 0.12 10.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/pathview.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'pathview' ...
** 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 'pathview' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathview' as pathview_1.16.5.zip
* DONE (pathview)