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BioC 2.13: CHECK report for metagenomeSeq on moscato1

This page was generated on 2014-04-05 09:51:18 -0700 (Sat, 05 Apr 2014).

Package 435/750HostnameOS / ArchBUILDCHECKBUILD BIN
metagenomeSeq 1.4.2
Joseph N. Paulson
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/metagenomeSeq
Last Changed Rev: 87795 / Revision: 88450
Last Changed Date: 2014-03-24 09:27:37 -0700 (Mon, 24 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: metagenomeSeq
Version: 1.4.2
Command: rm -rf metagenomeSeq.buildbin-libdir && mkdir metagenomeSeq.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metagenomeSeq.buildbin-libdir metagenomeSeq_1.4.2.tar.gz >metagenomeSeq-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=metagenomeSeq.buildbin-libdir --install="check:metagenomeSeq-install.out" --force-multiarch --no-vignettes --timings metagenomeSeq_1.4.2.tar.gz && mv metagenomeSeq.buildbin-libdir/* metagenomeSeq.Rcheck/ && rmdir metagenomeSeq.buildbin-libdir
StartedAt: 2014-04-05 05:03:49 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:06:30 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 160.3 seconds
RetCode: 0
Status:  OK  
CheckDir: metagenomeSeq.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/metagenomeSeq.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.4.2'
* 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
Packages in Depends field not imported from:
  'RColorBrewer' 'gplots' 'limma' 'matrixStats' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [33s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
fitZig 7.17   0.16    7.33
** running examples for arch 'x64' ... [35s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
fitZig 6.94   0.23    7.17
* 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-2.13-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
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

install for x64

* installing *source* package 'metagenomeSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metagenomeSeq' as metagenomeSeq_1.4.2.zip
* DONE (metagenomeSeq)

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

nameusersystemelapsed
MRcoefs1.650.091.74
MRcounts0.440.050.48
MRexperiment-class0.000.010.02
MRfisher1.350.051.40
MRfulltable3.130.033.16
MRtable1.300.031.33
cumNorm1.870.011.88
cumNormMat1.640.051.69
cumNormStat1.330.001.33
expSummary0.190.010.20
exportMat0.030.020.05
exportStats000
fitZig7.170.167.33
libSize0.550.060.61
load_meta0.090.000.09
load_metaQ0.000.010.02
load_phenoData000
newMRexperiment0.100.000.09
normFactors0.380.050.42
plotCorr2.730.092.83
plotGenus0.310.050.36
plotMRheatmap2.430.002.43
plotOTU0.320.010.36
plotOrd1.790.031.82
plotRare0.190.020.20
posterior.probs000
zigControl0.020.000.02

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

nameusersystemelapsed
MRcoefs1.420.001.42
MRcounts0.420.020.43
MRexperiment-class000
MRfisher1.210.011.23
MRfulltable3.720.023.73
MRtable1.350.081.43
cumNorm2.160.032.19
cumNormMat1.930.041.98
cumNormStat1.390.051.43
expSummary0.160.020.18
exportMat000
exportStats000
fitZig6.940.237.17
libSize0.340.050.39
load_meta0.040.000.04
load_metaQ000
load_phenoData000
newMRexperiment0.060.000.06
normFactors0.370.000.37
plotCorr2.780.112.89
plotGenus0.340.030.37
plotMRheatmap4.170.044.22
plotOTU0.420.020.43
plotOrd2.370.052.42
plotRare0.260.010.55
posterior.probs0.020.000.01
zigControl000