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BioC 3.0: CHECK report for metagenomeSeq on moscato1

This page was generated on 2015-04-10 09:48:48 -0700 (Fri, 10 Apr 2015).

Package 534/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.8.3
Joseph N. Paulson
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/metagenomeSeq
Last Changed Rev: 97784 / Revision: 102249
Last Changed Date: 2014-12-18 15:16:55 -0800 (Thu, 18 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: metagenomeSeq
Version: 1.8.3
Command: rm -rf metagenomeSeq.buildbin-libdir metagenomeSeq.Rcheck && mkdir metagenomeSeq.buildbin-libdir metagenomeSeq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeSeq.buildbin-libdir metagenomeSeq_1.8.3.tar.gz >metagenomeSeq.Rcheck\00install.out 2>&1 && cp metagenomeSeq.Rcheck\00install.out metagenomeSeq-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=metagenomeSeq.buildbin-libdir --install="check:metagenomeSeq-install.out" --force-multiarch --no-vignettes --timings metagenomeSeq_1.8.3.tar.gz
StartedAt: 2015-04-10 02:55:06 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:04:51 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 584.7 seconds
RetCode: 0
Status:  OK  
CheckDir: metagenomeSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf metagenomeSeq.buildbin-libdir metagenomeSeq.Rcheck && mkdir metagenomeSeq.buildbin-libdir metagenomeSeq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeSeq.buildbin-libdir metagenomeSeq_1.8.3.tar.gz >metagenomeSeq.Rcheck\00install.out 2>&1 && cp metagenomeSeq.Rcheck\00install.out metagenomeSeq-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=metagenomeSeq.buildbin-libdir --install="check:metagenomeSeq-install.out" --force-multiarch --no-vignettes --timings metagenomeSeq_1.8.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/metagenomeSeq.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metagenomeSeq/DESCRIPTION' ... OK
* this is package 'metagenomeSeq' version '1.8.3'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'metagenomeSeq' can be installed ... OK
* checking installed package size ... OK
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  'biom' 'gss'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcNormFactors: warning in colQuantiles(xx, p = p, na.rm = TRUE):
  partial argument match of 'p' to 'probs'
cumNormMat: warning in colQuantiles(xx, p = p, na.rm = TRUE): partial
  argument match of 'p' to 'probs'
exportStats: warning in colQuantiles(xx, p = p, na.rm = TRUE): partial
  argument match of 'p' to 'probs'
biom2MRexperiment: no visible global function definition for
  'biom_data'
biom2MRexperiment: no visible global function definition for
  'observation_metadata'
biom2MRexperiment: no visible global function definition for
  'sample_metadata'
fitDO: no visible global function definition for 'stopCluster'
fitPA: no visible global function definition for 'stopCluster'
load_biom: no visible global function definition for 'read_biom'
plotClassTimeSeries: no visible global function definition for
  'ssanova'
ssFit: no visible global function definition for 'ssanova'
ssPermAnalysis: no visible global function definition for 'ssanova'
* 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' ... [89s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
MRfulltable 1.31   0.03   13.15
fitDO       0.89   0.02   12.04
plotBubble  0.88   0.02   12.17
fitPA       0.53   0.08   10.83
** running examples for arch 'x64' ... [102s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
fitZig      6.09   0.08    6.16
MRfulltable 1.36   0.04   15.45
fitPA       0.85   0.08   14.87
fitDO       0.86   0.06   13.10
plotBubble  0.86   0.04   15.51
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [27s]
 [27s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [34s]
 [34s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/metagenomeSeq.Rcheck/00check.log'
for details.

metagenomeSeq.Rcheck/00install.out:


install for i386

* installing *source* package 'metagenomeSeq' ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
Creating a generic function for 'colSums' from package 'base' in package 'metagenomeSeq'
Creating a generic function for 'rowSums' from package 'base' in package 'metagenomeSeq'
Creating a generic function for 'rowMeans' from package 'base' in package 'metagenomeSeq'
Creating a generic function for 'colMeans' from package 'base' in package 'metagenomeSeq'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'metagenomeSeq' ...
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'metagenomeSeq' as metagenomeSeq_1.8.3.zip
* DONE (metagenomeSeq)

metagenomeSeq.Rcheck/examples_i386/metagenomeSeq-Ex.timings:

nameusersystemelapsed
MRcoefs2.030.032.10
MRcounts0.640.050.69
MRexperiment-class000
MRfulltable 1.31 0.0313.15
MRtable1.400.071.48
aggregateByTaxonomy000
biom2MRexperiment000
calcNormFactors1.180.051.23
correctIndices0.110.000.11
correlationTest0.320.000.31
cumNorm0.740.000.75
cumNormMat1.000.031.03
cumNormStat1.530.001.53
cumNormStatFast0.470.000.47
expSummary0.090.000.09
exportMat000
exportStats000
filterData0.220.000.22
fitDO 0.89 0.0212.04
fitPA 0.53 0.0810.83
fitSSTimeSeries1.450.031.97
fitTimeSeries1.390.001.39
fitZig4.310.114.41
libSize0.400.010.42
load_biom000
load_meta0.100.000.09
load_metaQ000
load_phenoData000
newMRexperiment0.080.000.08
normFactors0.450.060.51
plotBubble 0.88 0.0212.17
plotClassTimeSeries1.730.081.81
plotCorr1.260.001.26
plotFeature0.220.000.44
plotGenus0.260.000.26
plotMRheatmap4.120.064.18
plotOTU0.200.000.21
plotOrd0.590.020.60
plotRare0.130.010.14
plotTimeSeries1.190.021.21
posterior.probs000
ssFit000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz000
uniqueFeatures0.110.000.11
zigControl000

metagenomeSeq.Rcheck/examples_x64/metagenomeSeq-Ex.timings:

nameusersystemelapsed
MRcoefs2.510.112.65
MRcounts0.340.040.37
MRexperiment-class000
MRfulltable 1.36 0.0415.45
MRtable1.340.021.35
aggregateByTaxonomy000
biom2MRexperiment000
calcNormFactors1.220.031.25
correctIndices0.110.000.11
correlationTest0.170.010.19
cumNorm0.970.000.97
cumNormMat1.260.021.28
cumNormStat1.80.01.8
cumNormStatFast0.460.000.45
expSummary0.090.000.10
exportMat000
exportStats000
filterData0.220.020.23
fitDO 0.86 0.0613.10
fitPA 0.85 0.0814.87
fitSSTimeSeries1.800.042.26
fitTimeSeries1.320.021.35
fitZig6.090.086.16
libSize0.370.000.37
load_biom000
load_meta0.050.000.04
load_metaQ000
load_phenoData000
newMRexperiment0.060.000.07
normFactors0.340.030.37
plotBubble 0.86 0.0415.51
plotClassTimeSeries1.250.051.29
plotCorr1.100.021.19
plotFeature0.150.000.14
plotGenus0.170.010.19
plotMRheatmap3.600.033.65
plotOTU0.230.020.25
plotOrd0.720.010.73
plotRare0.090.000.10
plotTimeSeries1.470.071.53
posterior.probs000
ssFit000
ssIntervalCandidate000
ssPerm000
ssPermAnalysis000
trapz000
uniqueFeatures0.190.010.21
zigControl000