mmnet 1.11.2
Yang Cao , Fei Li
| Snapshot Date: 2016-09-14 19:15:30 -0700 (Wed, 14 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mmnet | | Last Changed Rev: 120838 / Revision: 120967 | | Last Changed Date: 2016-09-11 14:36:03 -0700 (Sun, 11 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mmnet_1.11.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/mmnet.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mmnet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mmnet’ version ‘1.11.2’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mmnet’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
data 2.2Mb
doc 3.0Mb
* 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
* 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
constructMetabolicNetwork: no visible binding for global variable
‘RefDbcache’
differentialAnalyzeNet : <anonymous>: no visible global function
definition for ‘wilcox.test’
estimateAbundance : estimateSingleAnno: no visible global function
definition for ‘aggregate’
generateMgrastWebsession: no visible global function definition for
‘read.delim’
getKOPathwayInfo: no visible global function definition for ‘na.omit’
getMgrastAnnotation : <anonymous>: no visible global function
definition for ‘flush.console’
getMgrastAnnotation: no visible global function definition for
‘read.delim’
loadMetabolicData: no visible global function definition for ‘data’
loadMetabolicData: no visible binding for global variable ‘RefDbcache’
make_biom: no visible global function definition for ‘packageVersion’
showMetagenomicNet : VertexColor: no visible global function definition
for ‘quantile’
submitMgrastJob : progressDown: no visible global function definition
for ‘flush.console’
uploadMgrast : progressDown: no visible global function definition for
‘flush.console’
Undefined global functions or variables:
RefDbcache aggregate data flush.console na.omit packageVersion
quantile read.delim wilcox.test
Consider adding
importFrom("stats", "aggregate", "na.omit", "quantile", "wilcox.test")
importFrom("utils", "data", "flush.console", "packageVersion",
"read.delim")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
showMetagenomicNet 37.352 0.264 37.629
topologicalAnalyzeNet 22.020 0.112 22.137
constructSSN 19.008 0.056 19.063
estimateAbundance 16.872 0.012 16.882
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/mmnet.Rcheck/00check.log’
for details.