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BioC 2.12: CHECK report for phyloseq on moscato2

This page was generated on 2013-10-09 09:39:05 -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: rm -rf phyloseq.buildbin-libdir && mkdir phyloseq.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phyloseq.buildbin-libdir phyloseq_1.4.5.tar.gz >phyloseq-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=phyloseq.buildbin-libdir --install="check:phyloseq-install.out" --force-multiarch --no-vignettes --timings phyloseq_1.4.5.tar.gz && mv phyloseq.buildbin-libdir/* phyloseq.Rcheck/ && rmdir phyloseq.buildbin-libdir
StartedAt: 2013-10-09 03:33:00 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 03:45:46 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 766.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: phyloseq.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/phyloseq.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'phyloseq' can be installed ... WARNING
Found the following significant warnings:
  Warning: package 'ape' was built under R version 3.0.2
  Warning: package 'ape' was built under R version 3.0.2
  Warning: package 'ape' was built under R version 3.0.2
See 'E:/biocbld/bbs-2.12-bioc/meat/phyloseq.Rcheck/00install.out' for details.
* 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
* 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 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [186s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
plot_scree            28.07   0.08   28.36
plot_tree             22.91   0.01   22.93
plot_ordination       18.06   0.27   18.35
data-soilrep          11.21   0.11   11.36
plot_richness         10.21   0.14   10.36
nodeplotblank          9.75   0.00    9.75
data-GlobalPatterns    7.94   0.06    8.02
data-enterotype        6.21   0.02    6.52
make_network           5.80   0.01    5.82
plot_phyloseq-methods  5.61   0.00    5.60
** running examples for arch 'x64' ... [221s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
plot_scree            36.27   0.26   36.55
plot_tree             30.92   0.04   30.95
plot_ordination       23.89   0.25   24.13
data-soilrep          12.32   0.19   12.53
plot_richness         11.31   0.16   11.47
nodeplotblank         10.97   0.02   10.99
data-GlobalPatterns    9.70   0.06    9.77
make_network           6.99   0.00    6.99
data-enterotype        6.24   0.03    6.27
plot_phyloseq-methods  5.99   0.01    6.01
rarefy_even_depth      5.97   0.03    6.00
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'testthat-phyloseq.R' [45s]
 [46s] OK
** running tests for arch 'x64'
  Running 'testthat-phyloseq.R' [54s]
 [54s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/phyloseq.Rcheck/00check.log'
for details.

phyloseq.Rcheck/00install.out:


install for i386

* installing *source* package 'phyloseq' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'ape' was built under R version 3.0.2
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: package 'ape' was built under R version 3.0.2
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

install for x64

* installing *source* package 'phyloseq' ...
** testing if installed package can be loaded
Warning: package 'ape' was built under R version 3.0.2
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
* MD5 sums
packaged installation of 'phyloseq' as phyloseq_1.4.5.zip
* DONE (phyloseq)