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BioC 3.5: CHECK report for CATALYST on tokay2

This page was generated on 2017-08-16 13:26:53 -0400 (Wed, 16 Aug 2017).

Package 175/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.1.1
Helena Lucia Crowell
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CATALYST
Last Changed Rev: 129568 / Revision: 131943
Last Changed Date: 2017-05-13 03:30:47 -0400 (Sat, 13 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CATALYST
Version: 1.1.1
Command: rm -rf CATALYST.buildbin-libdir CATALYST.Rcheck && mkdir CATALYST.buildbin-libdir CATALYST.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CATALYST.buildbin-libdir CATALYST_1.1.1.tar.gz >CATALYST.Rcheck\00install.out 2>&1 && cp CATALYST.Rcheck\00install.out CATALYST-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CATALYST.buildbin-libdir --install="check:CATALYST-install.out" --force-multiarch --no-vignettes --timings CATALYST_1.1.1.tar.gz
StartedAt: 2017-08-15 22:29:53 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:33:20 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 206.5 seconds
RetCode: 0
Status:  OK  
CheckDir: CATALYST.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CATALYST.buildbin-libdir CATALYST.Rcheck && mkdir CATALYST.buildbin-libdir CATALYST.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CATALYST.buildbin-libdir CATALYST_1.1.1.tar.gz >CATALYST.Rcheck\00install.out 2>&1 && cp CATALYST.Rcheck\00install.out CATALYST-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CATALYST.buildbin-libdir --install="check:CATALYST-install.out" --force-multiarch --no-vignettes --timings CATALYST_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CATALYST.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CATALYST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CATALYST' version '1.1.1'
* 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 whether package 'CATALYST' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    5.6Mb
* 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 ... OK
* 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' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
normCytof 9.73   0.04    9.86
estTrim   5.37   0.13    7.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
normCytof 11.79   0.05   11.83
plotMahal  5.52   0.00    5.51
estTrim    4.65   0.04    6.45
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/CATALYST.Rcheck/00check.log'
for details.


CATALYST.Rcheck/00install.out:


install for i386

* installing *source* package 'CATALYST' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'CATALYST' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CATALYST' as CATALYST_1.1.1.zip
* DONE (CATALYST)

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

nameusersystemelapsed
applyCutoffs2.210.012.22
assignPrelim1.510.001.51
compCytof1.640.001.64
computeSpillmat1.570.021.58
concatFCS0.050.000.04
data0.000.020.02
dbFrame-methods1.260.011.28
estCutoffs1.430.001.42
estTrim5.370.137.39
normCytof9.730.049.86
outFCS2.110.074.14
plotEvents2.720.012.74
plotMahal4.500.024.52
plotSpillmat1.640.011.66
plotYields2.350.032.38

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

nameusersystemelapsed
applyCutoffs2.600.032.62
assignPrelim1.790.011.81
compCytof1.950.001.95
computeSpillmat1.960.021.97
concatFCS0.060.000.06
data0.000.020.02
dbFrame-methods1.640.011.65
estCutoffs1.970.021.99
estTrim4.650.046.45
normCytof11.79 0.0511.83
outFCS4.100.064.17
plotEvents3.830.023.85
plotMahal5.520.005.51
plotSpillmat2.690.032.72
plotYields3.280.003.28