pathview 1.4.2
Weijun Luo
| 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/pathview | | Last Changed Rev: 92580 / Revision: 95116 | | Last Changed Date: 2014-07-16 20:02:24 -0700 (Wed, 16 Jul 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### rm -rf pathview.buildbin-libdir && mkdir pathview.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathview.buildbin-libdir pathview_1.4.2.tar.gz >pathview-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=pathview.buildbin-libdir --install="check:pathview-install.out" --force-multiarch --no-vignettes --timings pathview_1.4.2.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/pathview.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 'pathview/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathview' version '1.4.2'
* 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
Packages in Depends field not imported from:
'KEGGgraph' 'org.Hs.eg.db'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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'.
render.kegg.node: warning in sliced.shapes(plot.data$x + 0.5, height -
plot.data$y, plot.data$width/2 - 0.5, plot.data$height/2 - 0.25, col
= cols.ts, draw.border = F, shape = "rectangle"): partial argument
match of 'col' to 'cols'
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'
eg2id: no visible global function definition for 'biocLite'
id2eg: no visible global function definition for 'biocLite'
kegg.species.code: no visible binding for global variable 'korg'
keggview.graph: no visible binding for global variable
'KEGGEdgeSubtype'
keggview.graph: no visible binding for global variable 'nplot'
keggview.native: no visible binding for global variable 'nplot'
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 'cpd.accs'
sim.mol.data: no visible binding for global variable 'rn.list'
sim.mol.data: no visible binding for global variable 'ko.ids'
* 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' ... [44s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pathview 15.68 1.09 18.26
eg2id 6.20 0.06 11.24
** running examples for arch 'x64' ... [45s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pathview 18.75 1.54 21.71
eg2id 7.28 0.07 7.49
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [22s]
[22s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [24s]
[25s] 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
NOTE: There were 2 notes.
See
'E:/biocbld/bbs-2.14-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_1.4.2.zip
* DONE (pathview)