GOFunction 1.22.0
Jing Wang
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GOFunction | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### rm -rf GOFunction.buildbin-libdir GOFunction.Rcheck && mkdir GOFunction.buildbin-libdir GOFunction.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOFunction.buildbin-libdir GOFunction_1.22.0.tar.gz >GOFunction.Rcheck\00install.out 2>&1 && cp GOFunction.Rcheck\00install.out GOFunction-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=GOFunction.buildbin-libdir --install="check:GOFunction-install.out" --force-multiarch --no-vignettes --timings GOFunction_1.22.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/GOFunction.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOFunction/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GOFunction' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'Biobase' 'graph' 'Rgraphviz' 'GO.db' 'AnnotationDbi' 'SparseM'
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 'GOFunction' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'methods' 'Biobase' 'graph' 'Rgraphviz' 'GO.db' 'AnnotationDbi' 'SparseM'
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls to packages already attached by Depends:
'GO.db' 'Rgraphviz' 'SparseM' 'graph' 'methods'
Please remove these calls from your code.
Namespaces in Imports field not imported from:
'GO.db' 'Rgraphviz' 'graph'
All declared Imports should be used.
Packages in Depends field not imported from:
'GO.db' 'Rgraphviz' 'graph'
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 'GOFunction/R/zzz.R':
.onLoad calls:
require(methods)
Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
GOFunction: no visible global function definition for 'nodes'
GOFunction: no visible global function definition for 'write.csv'
createGODAG: no visible global function definition for 'sparseM2Graph'
createGODAG: no visible global function definition for 'graph2SparseM'
enrichmentFunction: no visible global function definition for 'phyper'
enrichmentFunction: no visible global function definition for
'p.adjust'
globalRedundancy : calculateEachTerm : calculateExtraTerm: no visible
global function definition for 'phyper'
localRedundancy: no visible global function definition for 'phyper'
showSigNodes: no visible global function definition for
'getDefaultAttrs'
showSigNodes: no visible global function definition for 'heat.colors'
showSigNodes: no visible global function definition for 'edgeWeights'
showSigNodes: no visible global function definition for 'nodes'
showSigNodes: no visible global function definition for 'bmp'
showSigNodes: no visible global function definition for 'plot'
showSigNodes: no visible global function definition for 'dev.off'
Undefined global functions or variables:
bmp dev.off edgeWeights getDefaultAttrs graph2SparseM heat.colors
nodes p.adjust phyper plot sparseM2Graph write.csv
Consider adding
importFrom("grDevices", "bmp", "dev.off", "heat.colors")
importFrom("graphics", "plot")
importFrom("stats", "p.adjust", "phyper")
importFrom("utils", "write.csv")
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
GOFunction 374.09 49.83 432.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
GOFunction 344.48 48.86 400.78
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/GOFunction.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'GOFunction' ...
** 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 'GOFunction' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOFunction' as GOFunction_1.22.0.zip
* DONE (GOFunction)