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BioC 2.14: CHECK report for QDNAseq on moscato2

This page was generated on 2014-10-08 08:56:35 -0700 (Wed, 08 Oct 2014).

Package 615/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QDNAseq 1.0.5
Ilari Scheinin
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/QDNAseq
Last Changed Rev: 91364 / Revision: 95116
Last Changed Date: 2014-06-13 04:48:35 -0700 (Fri, 13 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: QDNAseq
Version: 1.0.5
Command: rm -rf QDNAseq.buildbin-libdir && mkdir QDNAseq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QDNAseq.buildbin-libdir QDNAseq_1.0.5.tar.gz >QDNAseq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=QDNAseq.buildbin-libdir --install="check:QDNAseq-install.out" --force-multiarch --no-vignettes --timings QDNAseq_1.0.5.tar.gz
StartedAt: 2014-10-08 04:07:24 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 04:13:56 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 392.5 seconds
RetCode: 0
Status:  OK  
CheckDir: QDNAseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf QDNAseq.buildbin-libdir && mkdir QDNAseq.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QDNAseq.buildbin-libdir QDNAseq_1.0.5.tar.gz >QDNAseq-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=QDNAseq.buildbin-libdir --install="check:QDNAseq-install.out" --force-multiarch --no-vignettes --timings QDNAseq_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/QDNAseq.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QDNAseq/DESCRIPTION' ... OK
* this is package 'QDNAseq' version '1.0.5'
* 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 'QDNAseq' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'Biobase:::.showAnnotatedDataFrame'
  See the note in ?`:::` about the use of this operator.
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' ... [77s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
callBins               21.45   0.06   21.51
frequencyPlot          17.23   0.00   17.22
segmentBins             9.20   0.00    9.21
normalizeSegmentedBins  9.06   0.03    9.09
** running examples for arch 'x64' ... [67s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
callBins               17.91   0.04   17.96
frequencyPlot          16.69   0.05   16.74
normalizeSegmentedBins  6.92   0.06    6.99
segmentBins             6.83   0.00    6.83
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'QDNAseq,reproducibility.R' [9s]
  Running 'QDNAseq.R' [17s]
 [26s] OK
** running tests for arch 'x64' ...
  Running 'QDNAseq,reproducibility.R' [11s]
  Running 'QDNAseq.R' [18s]
 [29s] 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.14-bioc/meat/QDNAseq.Rcheck/00check.log'
for details.

QDNAseq.Rcheck/00install.out:


install for i386

* installing *source* package 'QDNAseq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'QDNAseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QDNAseq' as QDNAseq_1.0.5.zip
* DONE (QDNAseq)

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

nameusersystemelapsed
addPhenodata0.170.030.20
applyFilters0.380.000.37
binReadCounts000
callBins21.45 0.0621.51
compareToReference2.110.002.11
correctBins1.500.001.49
createBins000
estimateCorrection1.100.001.11
exportBins000
frequencyPlot17.23 0.0017.22
getBinAnnotations000
highlightFilters0.930.010.95
isobarPlot101
makeCgh1.440.001.44
noisePlot1.120.001.12
normalizeBins1.360.001.36
normalizeSegmentedBins9.060.039.09
plot1.650.001.65
poolRuns0.180.020.19
segmentBins9.200.009.21
smoothOutlierBins1.510.001.51

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

nameusersystemelapsed
addPhenodata0.170.000.17
applyFilters0.390.020.40
binReadCounts000
callBins17.91 0.0417.96
compareToReference1.330.001.33
correctBins1.080.031.10
createBins000
estimateCorrection0.920.000.92
exportBins000
frequencyPlot16.69 0.0516.74
getBinAnnotations000
highlightFilters0.790.020.81
isobarPlot0.880.010.89
makeCgh1.240.021.27
noisePlot0.960.000.95
normalizeBins1.030.001.03
normalizeSegmentedBins6.920.066.99
plot1.360.001.35
poolRuns0.170.000.18
segmentBins6.830.006.83
smoothOutlierBins1.030.031.06