phyloseq 1.0.3
Paul J. McMurdie
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/phyloseq | | Last Changed Rev: 69344 / Revision: 69725 | | Last Changed Date: 2012-09-11 17:07:57 -0700 (Tue, 11 Sep 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/phyloseq.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phyloseq/DESCRIPTION’ ... OK
* this is package ‘phyloseq’ version ‘1.0.3’
* 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 whether package ‘phyloseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
JSD: no visible binding for global variable ‘i’
export_env_file: no visible global function definition for ‘ps’
fastUniFrac: no visible binding for global variable ‘i’
filter_taxa: no visible binding for global variable ‘enterotype’
filter_taxa: no visible binding for global variable ‘expr’
originalUniFrac: no visible binding for global variable ‘i’
otu2df : trimdf: no visible binding for global variable ‘TaxaGroup’
otu2df : trimdf: no visible binding for global variable ‘Abundance’
plot_richness_estimates: no visible binding for global variable ‘value’
plot_richness_estimates: no visible binding for global variable ‘se’
plot_sample_network: no visible binding for global variable ‘x’
plot_sample_network: no visible binding for global variable ‘y’
plot_taxa_bar: no visible binding for global variable ‘Abundance’
taxaplot: no visible binding for global variable ‘Abundance’
* 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:
‘naturemag.bst’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/phyloseq.Rcheck/00check.log’
for details.
* installing *source* package ‘phyloseq’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’ and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
‘phyloseq_analysis.Rnw’
‘phyloseq_basics.Rnw’
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “pipe” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “textConnection” in package ‘BiocGenerics’ seems equivalent to one from package ‘RJSONIO’ and is not turning on duplicate class definitions for this class
* DONE (phyloseq)