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BioC 3.3: CHECK report for PCAN on moscato2

This page was generated on 2016-10-13 12:54:59 -0700 (Thu, 13 Oct 2016).

Package 842/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PCAN 1.0.2
Matthew Page and Patrice Godard
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/PCAN
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
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
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PCAN
Version: 1.0.2
Command: rm -rf PCAN.buildbin-libdir PCAN.Rcheck && mkdir PCAN.buildbin-libdir PCAN.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCAN.buildbin-libdir PCAN_1.0.2.tar.gz >PCAN.Rcheck\00install.out 2>&1 && cp PCAN.Rcheck\00install.out PCAN-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=PCAN.buildbin-libdir --install="check:PCAN-install.out" --force-multiarch --no-vignettes --timings PCAN_1.0.2.tar.gz
StartedAt: 2016-10-13 07:11:47 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 07:21:58 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 610.9 seconds
RetCode: 0
Status:  OK  
CheckDir: PCAN.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PCAN.buildbin-libdir PCAN.Rcheck && mkdir PCAN.buildbin-libdir PCAN.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PCAN.buildbin-libdir PCAN_1.0.2.tar.gz >PCAN.Rcheck\00install.out 2>&1 && cp PCAN.Rcheck\00install.out PCAN-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=PCAN.buildbin-libdir --install="check:PCAN-install.out" --force-multiarch --no-vignettes --timings PCAN_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/PCAN.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PCAN/DESCRIPTION' ... OK
* this is package 'PCAN' version '1.0.2'
* 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 'PCAN' 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 ... 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
hpGeneListComp   68.66   0.18   68.97
hpGeneHeatmap    65.76   0.23   65.99
compareHPSets    64.89   0.18   65.07
hpSetCompSummary  5.47   0.05    5.54
traitDef          5.42   0.02    5.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
compareHPSets  95.19   0.14   95.33
hpGeneHeatmap  91.68   0.14   91.82
hpGeneListComp 72.20   0.14   72.34
geneDef         6.06   0.02    6.08
hpByTrait       5.68   0.04    5.72
traitDef        5.43   0.03    5.48
* 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: OK

PCAN.Rcheck/00install.out:


install for i386

* installing *source* package 'PCAN' ...
** 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 'PCAN' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PCAN' as PCAN_1.0.2.zip
* DONE (PCAN)

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

nameusersystemelapsed
calcHpSim3.640.033.66
compareHPSets64.89 0.1865.07
computeHpIC2.760.072.82
geneByHp2.770.002.78
geneByTrait0.050.000.05
geneDef4.310.014.32
hpByTrait4.500.084.58
hpDef4.040.034.07
hpGeneHeatmap65.76 0.2365.99
hpGeneListComp68.66 0.1868.97
hpSetCompBestMatch4.910.014.93
hpSetCompSummary5.470.055.54
hp_ancestors4.580.044.61
hp_class0.070.000.07
hp_descendants3.050.013.06
hqStrNw000
hsEntrezByRPath000
rPath000
traitDef5.420.025.45

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

nameusersystemelapsed
calcHpSim3.490.063.56
compareHPSets95.19 0.1495.33
computeHpIC4.420.054.46
geneByHp3.490.013.52
geneByTrait0.070.000.06
geneDef6.060.026.08
hpByTrait5.680.045.72
hpDef4.030.074.09
hpGeneHeatmap91.68 0.1491.82
hpGeneListComp72.20 0.1472.34
hpSetCompBestMatch4.940.014.96
hpSetCompSummary4.460.054.51
hp_ancestors4.060.024.07
hp_class0.090.000.10
hp_descendants3.980.034.00
hqStrNw000
hsEntrezByRPath000
rPath000
traitDef5.430.035.48