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BioC 3.2: CHECK report for SEPA on moscato1

This page was generated on 2016-04-23 10:22:03 -0700 (Sat, 23 Apr 2016).

Package 953/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SEPA 1.0.0
Zhicheng Ji
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SEPA
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SEPA
Version: 1.0.0
Command: rm -rf SEPA.buildbin-libdir SEPA.Rcheck && mkdir SEPA.buildbin-libdir SEPA.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SEPA.buildbin-libdir SEPA_1.0.0.tar.gz >SEPA.Rcheck\00install.out 2>&1 && cp SEPA.Rcheck\00install.out SEPA-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SEPA.buildbin-libdir --install="check:SEPA-install.out" --force-multiarch --no-vignettes --timings SEPA_1.0.0.tar.gz
StartedAt: 2016-04-23 07:20:31 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 07:48:32 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1681.1 seconds
RetCode: 0
Status:  OK  
CheckDir: SEPA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SEPA.buildbin-libdir SEPA.Rcheck && mkdir SEPA.buildbin-libdir SEPA.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SEPA.buildbin-libdir SEPA_1.0.0.tar.gz >SEPA.Rcheck\00install.out 2>&1 && cp SEPA.Rcheck\00install.out SEPA-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SEPA.buildbin-libdir --install="check:SEPA-install.out" --force-multiarch --no-vignettes --timings SEPA_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/SEPA.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SEPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SEPA' version '1.0.0'
* 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 'SEPA' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
pseudotimevisualize: no visible binding for global variable
  'pseudotime'
pseudotimevisualize: no visible binding for global variable 'Var2'
pseudotimevisualize: no visible binding for global variable 'Var1'
pseudotimevisualize: no visible binding for global variable 'value'
pseudotimevisualize: no visible binding for global variable 'xend'
pseudotimevisualize: no visible binding for global variable 'yend'
truetimevisualize: no visible binding for global variable 'expmean'
truetimevisualize: no visible binding for global variable 'Gene'
windowGOvisualize: no visible binding for global variable 'Var1'
windowGOvisualize: no visible binding for global variable 'value'
* 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' ... [11m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
windowGOvisualize   157.54   0.63  160.73
windowGOanalysis    153.49   0.35  155.45
pseudotimevisualize 115.18   0.07  115.24
patternGOanalysis   100.77   0.99  115.50
pseudotimepattern   100.68   0.25  100.94
** running examples for arch 'x64' ... [14m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
windowGOvisualize   196.06   0.41  197.65
windowGOanalysis    195.36   0.47  199.48
pseudotimepattern   144.88   0.34  145.24
pseudotimevisualize 144.85   0.01  144.86
patternGOanalysis   116.25   0.80  120.53
* 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
  'D:/biocbld/bbs-3.2-bioc/meat/SEPA.Rcheck/00check.log'
for details.


SEPA.Rcheck/00install.out:


install for i386

* installing *source* package 'SEPA' ...
** 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 'SEPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SEPA' as SEPA_1.0.0.zip
* DONE (SEPA)

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

nameusersystemelapsed
SEPAui000
patternGOanalysis100.77 0.99115.50
patternsummary1.590.001.59
pseudotimepattern100.68 0.25100.94
pseudotimevisualize115.18 0.07115.24
truetimepattern1.360.001.36
truetimevisualize0.320.000.33
windowGOanalysis153.49 0.35155.45
windowGOvisualize157.54 0.63160.73

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

nameusersystemelapsed
SEPAui000
patternGOanalysis116.25 0.80120.53
patternsummary2.90.02.9
pseudotimepattern144.88 0.34145.24
pseudotimevisualize144.85 0.01144.86
truetimepattern2.150.002.15
truetimevisualize0.380.000.37
windowGOanalysis195.36 0.47199.48
windowGOvisualize196.06 0.41197.65