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BioC 3.1: CHECK report for macat on moscato2

This page was generated on 2015-10-09 09:27:21 -0700 (Fri, 09 Oct 2015).

Package 541/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
macat 1.42.0
Joern Toedling
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/macat
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: macat
Version: 1.42.0
Command: rm -rf macat.buildbin-libdir macat.Rcheck && mkdir macat.buildbin-libdir macat.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=macat.buildbin-libdir macat_1.42.0.tar.gz >macat.Rcheck\00install.out 2>&1 && cp macat.Rcheck\00install.out macat-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=macat.buildbin-libdir --install="check:macat-install.out" --force-multiarch --no-vignettes --timings macat_1.42.0.tar.gz
StartedAt: 2015-10-09 03:20:44 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:24:23 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 218.5 seconds
RetCode: 0
Status:  OK  
CheckDir: macat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf macat.buildbin-libdir macat.Rcheck && mkdir macat.buildbin-libdir macat.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=macat.buildbin-libdir macat_1.42.0.tar.gz >macat.Rcheck\00install.out 2>&1 && cp macat.Rcheck\00install.out macat-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=macat.buildbin-libdir --install="check:macat-install.out" --force-multiarch --no-vignettes --timings macat_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/macat.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 'macat/DESCRIPTION' ... OK
* this is package 'macat' version '1.42.0'
* 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 'macat' 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 'annotate' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'annotate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'annotate:::getTDRows'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalScoring : computePermSlideScores: warning in compute.sliding(permM,
  chrom = chromosome, sample = 1, kernel, kernelparams, step.width =
  step.width): partial argument match of 'chrom' to 'chromosome'
preprocessedLoader: warning in require(chip, character.only = TRUE,
  quiet = TRUE): partial argument match of 'quiet' to 'quietly'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
buildMACAT: no visible global function definition for 'featureNames'
buildMACAT: no visible global function definition for 'sampleNames'
buildMACAT: no visible global function definition for 'exprs'
preprocessedLoader: no visible global function definition for
  'buildChromLocation'
preprocessedLoader: no visible global function definition for 'pData<-'
preprocessedLoader: no visible global function definition for
  'varLabels<-'
preprocessedLoader: no visible global function definition for
  'chromLocs'
preprocessedLoader : usedChromGenes2: no visible global function
  definition for 'chromLocs'
preprocessedLoader : usedChromGenes2: no visible global function
  definition for 'featureNames'
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [47s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
discretize_tscores 23.48   0.01   23.69
get_results         9.73   0.00    9.73
** running examples for arch 'x64' ... [65s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
discretize_tscores 33.37   0.03   33.40
get_results        15.17   0.03   15.19
* 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/macat.Rcheck/00check.log'
for details.


macat.Rcheck/00install.out:


install for i386

* installing *source* package 'macat' ...
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'macat' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'macat' as macat_1.42.0.zip
* DONE (macat)

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

nameusersystemelapsed
buildMACAT1.480.031.51
compute_sliding1.670.021.69
discreteKernelize1.340.001.34
discretizeAll000
discretize_tscores23.48 0.0123.69
evalScoring303
evaluateParameters0.650.000.65
get_results9.730.009.73
kernelize0.480.000.60
kernelizeAll000
kernelizeToPython000
kernels0.020.000.12
loaddatapkg000
plot_MACATevalScoring000
preprocessedLoader000
pythondata000
scoring0.030.000.03
stjd0.030.000.03

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

nameusersystemelapsed
buildMACAT1.830.011.84
compute_sliding2.660.052.71
discreteKernelize2.060.002.06
discretizeAll000
discretize_tscores33.37 0.0333.40
evalScoring4.130.034.17
evaluateParameters0.990.000.98
get_results15.17 0.0315.19
kernelize0.810.020.83
kernelizeAll000
kernelizeToPython000
kernels0.010.000.01
loaddatapkg000
plot_MACATevalScoring000
preprocessedLoader000
pythondata000
scoring0.010.000.01
stjd0.020.000.02