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BioC 3.1: CHECK report for alsace on moscato2

This page was generated on 2015-10-09 09:31:00 -0700 (Fri, 09 Oct 2015).

Package 35/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alsace 1.4.0
Ron Wehrens
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/alsace
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: alsace
Version: 1.4.0
Command: rm -rf alsace.buildbin-libdir alsace.Rcheck && mkdir alsace.buildbin-libdir alsace.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=alsace.buildbin-libdir alsace_1.4.0.tar.gz >alsace.Rcheck\00install.out 2>&1 && cp alsace.Rcheck\00install.out alsace-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=alsace.buildbin-libdir --install="check:alsace-install.out" --force-multiarch --no-vignettes --timings alsace_1.4.0.tar.gz
StartedAt: 2015-10-08 23:16:04 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:18:09 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 124.4 seconds
RetCode: 0
Status:  OK  
CheckDir: alsace.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf alsace.buildbin-libdir alsace.Rcheck && mkdir alsace.buildbin-libdir alsace.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=alsace.buildbin-libdir alsace_1.4.0.tar.gz >alsace.Rcheck\00install.out 2>&1 && cp alsace.Rcheck\00install.out alsace-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=alsace.buildbin-libdir --install="check:alsace-install.out" --force-multiarch --no-vignettes --timings alsace_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/alsace.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'alsace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'alsace' version '1.4.0'
* 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 'alsace' 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
'library' or 'require' call to 'lattice' 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 ... NOTE
getPeakTable : clusterPeaks: no visible global function definition for
  'stripplot'
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for 'panel.stripplot'
getPeakTable : clusterPeaks : <anonymous>: no visible global function
  definition for 'panel.abline'
* 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' ... [43s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
components   13.54      0   13.54
teaMerged     6.28      0    6.31
correctPeaks  5.59      0    5.59
** running examples for arch 'x64' ... [48s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
components   14.13      0   14.13
correctPeaks  7.30      0    7.30
teaMerged     6.60      0    6.60
fitpeaks      5.04      0    5.04
* 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: 2 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/alsace.Rcheck/00check.log'
for details.


alsace.Rcheck/00install.out:


install for i386

* installing *source* package 'alsace' ...
** 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 'alsace' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'alsace' as alsace_1.4.0.zip
* DONE (alsace)

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

nameusersystemelapsed
components13.54 0.0013.54
correctPeaks5.590.005.59
correctRT2.820.012.83
doALS4.530.004.53
filterPeaks0.050.000.05
fitpeaks4.310.004.31
getAllPeaks0.040.000.04
getPeakTable3.080.003.09
opa1.790.001.81
preprocess0.170.000.17
showALSresult0.170.000.18
tea0.210.000.24
teaMerged6.280.006.31
windows0.140.020.15

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

nameusersystemelapsed
components14.13 0.0014.13
correctPeaks7.30.07.3
correctRT3.500.013.51
doALS4.930.024.95
filterPeaks0.060.000.06
fitpeaks5.040.005.04
getAllPeaks0.110.000.11
getPeakTable3.570.003.60
opa1.780.002.09
preprocess0.140.000.14
showALSresult0.140.010.16
tea0.120.020.14
teaMerged6.60.06.6
windows0.190.000.18