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BioC 2.12: CHECK report for phyloseq on petty

This page was generated on 2013-10-09 09:40:08 -0700 (Wed, 09 Oct 2013).

Package 480/671HostnameOS / ArchBUILDCHECKBUILD BIN
phyloseq 1.4.5
Paul J. McMurdie
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/phyloseq
Last Changed Rev: 80531 / Revision: 81334
Last Changed Date: 2013-09-17 16:32:32 -0700 (Tue, 17 Sep 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: phyloseq
Version: 1.4.5
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phyloseq_1.4.5.tar.gz
StartedAt: 2013-10-08 23:26:03 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:36:39 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 635.4 seconds
RetCode: 0
Status:  OK 
CheckDir: phyloseq.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/phyloseq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'phyloseq/DESCRIPTION' ... OK
* this is package 'phyloseq' version '1.4.5'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'phyloseq' can be installed ... [28s/29s] OK
* checking installed package size ... OK
* checking package 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 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'
fastUniFrac: no visible binding for global variable 'i'
import_qiime_otu_tax: no visible binding for global variable 'i'
nodeplotboot : <anonymous>: no visible binding for global variable 'x'
nodeplotboot : <anonymous>: no visible binding for global variable 'y'
nodeplotdefault : <anonymous>: no visible binding for global variable
  'x'
nodeplotdefault : <anonymous>: no visible binding for global variable
  'y'
nodeplotdefault : <anonymous>: no visible binding for global variable
  'label'
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_heatmap: no visible binding for global variable 'x'
plot_heatmap: no visible binding for global variable 'y'
plot_heatmap: no visible binding for global variable 'value'
plot_network: no visible binding for global variable 'x'
plot_network: no visible binding for global variable 'y'
plot_richness: no visible binding for global variable 'variable'
plot_richness: no visible binding for global variable 'value'
plot_richness: no visible binding for global variable 'se'
plot_richness_estimates: no visible binding for global variable
  'variable'
plot_richness_estimates: no visible binding for global variable 'value'
plot_richness_estimates: no visible binding for global variable 'se'
plot_scree: no visible binding for global variable 'eigenvalue'
plot_taxa_bar: no visible binding for global variable 'Abundance'
plot_tree_only: no visible binding for global variable 'x'
plot_tree_only: no visible binding for global variable 'y'
plot_tree_only: no visible binding for global variable 'xend'
plot_tree_only: no visible binding for global variable 'yend'
plot_tree_sampledodge: no visible binding for global variable 'value'
plot_tree_sampledodge: no visible binding for global variable 'x'
plot_tree_sampledodge: no visible binding for global variable 'x.adj'
plot_tree_sampledodge: no visible binding for global variable 'y'
plot_tree_sampledodge: no visible binding for global variable
  'tipLabels'
taxaplot: no visible binding for global variable 'Abundance'
merge_phyloseq_pair,sample_data-sample_data : <anonymous>: no visible
  binding for global variable 'X0'
plot_phyloseq,phyloseq: no visible binding for global variable
  'esophagus'
* 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 examples ... [276s/281s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_scree            43.269  5.590  49.246
plot_tree             33.537  0.460  34.677
plot_ordination       26.854  2.811  30.020
data-soilrep          14.906  1.129  16.624
plot_richness         12.470  2.176  14.749
data-GlobalPatterns   12.107  1.408  13.710
nodeplotblank         12.691  0.167  13.049
data-enterotype        8.560  0.224   9.030
make_network           7.368  0.140   7.588
rarefy_even_depth      7.106  0.379   7.525
plot_phyloseq-methods  7.081  0.114   7.218
threshrank             4.761  1.816   6.883
plot_bar               6.299  0.277   6.714
plot_network           6.044  0.098   6.159
merge_samples-methods  5.331  0.454   5.827
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'testthat-phyloseq.R' [68s/70s]
 [69s/71s] 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 was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/phyloseq.Rcheck/00check.log'
for details.

phyloseq.Rcheck/00install.out:

* installing *source* package 'phyloseq' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics' and is not turning on duplicate class definitions for this class
* DONE (phyloseq)

phyloseq.Rcheck/phyloseq-Ex.timings:

nameusersystemelapsed
DPCoA0.0150.0030.020
JSD0.0100.0010.011
UniFrac-methods0.0350.0020.038
access0.0100.0010.009
assign-otu_table0.0140.0010.016
assign-phy_tree0.0190.0010.020
assign-sample_data0.0190.0010.021
assign-sample_names0.0460.0070.052
assign-tax_table0.0200.0010.022
assign-taxa_are_rows0.2920.0020.295
assign-taxa_names0.0380.0140.053
build_tax_table0.0650.0040.070
cca-rda-phyloseq-methods0.0120.0040.016
data-GlobalPatterns12.107 1.40813.710
data-enterotype8.5600.2249.030
data-esophagus3.5120.0603.595
data-soilrep14.906 1.12916.624
distance2.9320.0423.298
edgelist2clique0.0030.0030.006
envHash2otu_table0.0030.0050.008
estimate_richness1.7080.2791.997
export_env_file0.0020.0040.005
export_mothur_dist0.0030.0020.005
filter_taxa2.0460.1292.194
filterfun_sample0.0520.0080.061
genefilter_sample-methods0.0030.0050.010
get.component.classes0.0020.0040.006
get_sample-methods0.0080.0110.019
get_taxa-methods0.0090.0100.019
get_taxa_unique0.4130.0590.480
get_variable0.7060.0410.752
getslots.phyloseq0.3540.0370.395
import0.0020.0010.003
import_RDP_otu1.7050.0381.748
import_biom0.1870.0410.249
import_env_file0.0020.0020.003
import_mothur0.0100.0090.018
import_mothur_dist0.0030.0050.008
import_pyrotagger_tab0.0020.0030.005
import_qiime1.2820.0311.324
import_qiime_otu_tax1.0290.0841.124
import_qiime_sample_data0.0530.0070.059
index_reorder0.0020.0020.005
intersect_taxa0.0020.0050.007
make_network7.3680.1407.588
merge_phyloseq0.0090.0060.015
merge_phyloseq_pair-methods0.0100.0090.020
merge_samples-methods5.3310.4545.827
merge_taxa-methods3.0910.0573.191
mt-methods0.0040.0060.009
nodeplotblank12.691 0.16713.049
nodeplotboot0.0030.0040.007
nodeplotdefault0.0020.0030.006
nsamples-methods0.0070.0070.015
ntaxa-methods0.0030.0050.008
ordinate0.0120.0140.026
otu_table-methods0.0020.0020.005
parseTaxonomy-functions0.0110.0110.023
phy_tree-methods0.3370.0320.370
phyloseq0.0630.0250.087
plot-taxa-bar4.6680.2754.974
plot_bar6.2990.2776.714
plot_heatmap3.8430.3124.174
plot_network6.0440.0986.159
plot_ordination26.854 2.81130.020
plot_phyloseq-methods7.0810.1147.218
plot_richness12.470 2.17614.749
plot_scree43.269 5.59049.246
plot_tree33.537 0.46034.677
prune_samples-methods1.4450.3141.783
prune_taxa-methods0.0960.0270.125
psmelt2.1080.3452.478
rank_names0.0410.0180.059
rarefy_even_depth7.1060.3797.525
read_tree0.3140.0080.323
reconcile_categories0.0130.0050.019
refseq-methods0.3450.0310.377
rm_outlierf0.0720.0130.085
sample_data-methods0.0030.0040.007
sample_names-methods0.0030.0050.007
sample_sums0.0510.0260.077
sample_variables0.0430.0120.055
show-methods0.0020.0040.005
splat.phyloseq.objects0.0120.0040.016
subset_ord_plot0.0110.0040.016
subset_samples-methods0.0020.0030.005
subset_taxa-methods0.0020.0020.004
tax_glom0.0040.0040.007
tax_table-methods0.0020.0030.006
taxa_names-methods0.0030.0040.007
taxa_sums0.0510.0330.084
threshrank4.7611.8166.883
threshrankfun0.1550.0400.196
tip_glom-methods0.0120.0080.021
topf0.0440.0090.053
topk0.0470.0210.069
topp0.0440.0090.053
transformcounts0.2540.0690.346
transpose-methods1.1150.9742.496
tree.get.tags0.0110.0120.024
tree.has.tags0.0030.0040.007