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BioC 3.2: CHECK report for metagenomeSeq on zin1

This page was generated on 2016-04-23 10:12:59 -0700 (Sat, 23 Apr 2016).

Package 623/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metagenomeSeq 1.12.1
Joseph N. Paulson
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/metagenomeSeq
Last Changed Rev: 116422 / Revision: 116712
Last Changed Date: 2016-04-17 13:10:43 -0700 (Sun, 17 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: metagenomeSeq
Version: 1.12.1
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.12.1.tar.gz
StartedAt: 2016-04-23 02:41:08 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:43:00 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 111.5 seconds
RetCode: 0
Status:  OK 
CheckDir: metagenomeSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings metagenomeSeq_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.12.1’
* 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 ‘metagenomeSeq’ can be installed ... [6s/6s] 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
* 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' call to ‘biom’ in package code.
  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 ... OK
* 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 ... [28s/36s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [11s/11s] 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/metagenomeSeq.Rcheck/00check.log’
for details.


metagenomeSeq.Rcheck/00install.out:

* installing *source* package ‘metagenomeSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (metagenomeSeq)

metagenomeSeq.Rcheck/metagenomeSeq-Ex.timings:

nameusersystemelapsed
MRcoefs1.7530.0561.808
MRcounts0.3400.0120.352
MRexperiment-class0.0000.0000.001
MRfulltable1.1560.0281.186
MRtable1.2480.0001.255
aggregateBySample0.1760.0040.180
aggregateByTaxonomy0.1470.0040.151
biom2MRexperiment0.0010.0000.000
calcNormFactors0.7140.0080.722
correctIndices0.1300.0040.133
correlationTest0.2810.0000.282
cumNorm0.5880.0040.591
cumNormMat0.6310.0040.635
cumNormStat1.0330.0081.043
cumNormStatFast0.3940.0080.419
expSummary0.1110.0030.114
exportMat0.0010.0000.000
exportStats000
filterData0.3140.0000.314
fitDO0.5400.0173.283
fitFeatureModel1.2930.0441.336
fitPA0.4450.0253.037
fitSSTimeSeries1.4720.0401.510
fitTimeSeries1.2050.0081.212
fitZig2.7290.0442.772
libSize0.3390.0160.351
load_biom0.0000.0000.001
load_meta0.0280.0000.029
load_metaQ0.0010.0000.000
load_phenoData0.0000.0000.001
newMRexperiment0.0420.0000.042
normFactors0.3480.0080.361
plotBubble0.7160.0333.236
plotClassTimeSeries1.2000.0081.207
plotCorr0.6640.0000.663
plotFeature0.1860.0040.189
plotGenus0.1780.0000.178
plotMRheatmap2.3340.0042.339
plotOTU0.1610.0040.166
plotOrd0.3860.0000.385
plotRare0.1490.0000.149
plotTimeSeries1.2130.0001.214
posteriorProbs0.0000.0000.001
returnAppropriateObj0.3470.0080.356
ssFit0.0000.0000.001
ssIntervalCandidate000
ssPerm0.0000.0000.001
ssPermAnalysis000
trapz0.0020.0000.001
uniqueFeatures0.140.000.14
zigControl000