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BioC 3.5: CHECK report for CountClust on tokay2

This page was generated on 2017-08-16 13:25:34 -0400 (Wed, 16 Aug 2017).

Package 287/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CountClust 1.2.0
Kushal Dey
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/CountClust
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK NO, built version is LOWER than in internal repository!!!
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK NO, built version is LOWER than 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: CountClust
Version: 1.2.0
Command: rm -rf CountClust.buildbin-libdir CountClust.Rcheck && mkdir CountClust.buildbin-libdir CountClust.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CountClust.buildbin-libdir CountClust_1.2.0.tar.gz >CountClust.Rcheck\00install.out 2>&1 && cp CountClust.Rcheck\00install.out CountClust-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CountClust.buildbin-libdir --install="check:CountClust-install.out" --force-multiarch --no-vignettes --timings CountClust_1.2.0.tar.gz
StartedAt: 2017-08-15 22:59:55 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:04:00 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 244.6 seconds
RetCode: 0
Status:  OK  
CheckDir: CountClust.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CountClust.buildbin-libdir CountClust.Rcheck && mkdir CountClust.buildbin-libdir CountClust.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CountClust.buildbin-libdir CountClust_1.2.0.tar.gz >CountClust.Rcheck\00install.out 2>&1 && cp CountClust.Rcheck\00install.out CountClust-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=CountClust.buildbin-libdir --install="check:CountClust-install.out" --force-multiarch --no-vignettes --timings CountClust_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/CountClust.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 'CountClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CountClust' version '1.2.0'
* package encoding: UTF-8
* 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 'CountClust' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data  17.5Mb
* 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' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ExtractHighCorFeatures 14.79   0.30   15.33
compGoM                 7.18   0.44    7.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ExtractHighCorFeatures 18.89   0.24   19.37
compGoM                 8.55   0.67    9.38
StructureGGplot         5.81   0.08    6.09
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/CountClust.Rcheck/00check.log'
for details.


CountClust.Rcheck/00install.out:


install for i386

* installing *source* package 'CountClust' ...
** 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 'CountClust' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CountClust' as CountClust_1.2.0.zip
* DONE (CountClust)

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

nameusersystemelapsed
BatchCorrectedCounts0.720.020.74
ExtractHighCorFeatures14.79 0.3015.33
ExtractTopFeatures2.400.142.53
FitGoM1.200.151.36
FitGoMpool2.170.252.42
RemoveSparseFeatures000
StructureGGplot4.450.174.83
Structure_omega000
cg_topics0.390.070.45
compGoM7.180.447.62
compare_omega0.030.000.03
handleNA000
nullmodel_GoM2.450.032.49

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

nameusersystemelapsed
BatchCorrectedCounts0.870.000.88
ExtractHighCorFeatures18.89 0.2419.37
ExtractTopFeatures2.540.202.73
FitGoM1.390.141.54
FitGoMpool2.110.312.42
RemoveSparseFeatures000
StructureGGplot5.810.086.09
Structure_omega000
cg_topics0.650.050.70
compGoM8.550.679.38
compare_omega0.040.000.04
handleNA0.020.000.02
nullmodel_GoM2.700.052.75