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BioC 3.3: CHECK report for CoCiteStats on moscato2

This page was generated on 2016-10-13 12:47:30 -0700 (Thu, 13 Oct 2016).

Package 222/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoCiteStats 1.44.0
Bioconductor Package Maintainer
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/CoCiteStats
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 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: CoCiteStats
Version: 1.44.0
Command: rm -rf CoCiteStats.buildbin-libdir CoCiteStats.Rcheck && mkdir CoCiteStats.buildbin-libdir CoCiteStats.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoCiteStats.buildbin-libdir CoCiteStats_1.44.0.tar.gz >CoCiteStats.Rcheck\00install.out 2>&1 && cp CoCiteStats.Rcheck\00install.out CoCiteStats-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CoCiteStats.buildbin-libdir --install="check:CoCiteStats-install.out" --force-multiarch --no-vignettes --timings CoCiteStats_1.44.0.tar.gz
StartedAt: 2016-10-13 02:22:40 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 02:32:02 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 562.0 seconds
RetCode: 0
Status:  OK  
CheckDir: CoCiteStats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CoCiteStats.buildbin-libdir CoCiteStats.Rcheck && mkdir CoCiteStats.buildbin-libdir CoCiteStats.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CoCiteStats.buildbin-libdir CoCiteStats_1.44.0.tar.gz >CoCiteStats.Rcheck\00install.out 2>&1 && cp CoCiteStats.Rcheck\00install.out CoCiteStats-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=CoCiteStats.buildbin-libdir --install="check:CoCiteStats-install.out" --force-multiarch --no-vignettes --timings CoCiteStats_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/CoCiteStats.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 'CoCiteStats/DESCRIPTION' ... OK
* this is package 'CoCiteStats' version '1.44.0'
* 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 'CoCiteStats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: 'org.Hs.eg.db'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gene.geneslist.sig: no visible global function definition for 'Lkeys'
gene.geneslist.sig: no visible binding for global variable
  'org.Hs.egPMID'
paperLen: no visible global function definition for 'toTable'
paperLen: no visible binding for global variable 'org.Hs.egPMID'
paperLen: no visible global function definition for 'nhit'
paperLen: no visible global function definition for 'revmap'
Undefined global functions or variables:
  Lkeys nhit org.Hs.egPMID revmap toTable
* checking Rd files ... NOTE
prepare_Rd: gene.geneslist.statistic.Rd:19-21: Dropping empty section \details
* 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 examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
actorAdjTable            35.84   3.40   42.70
gene.geneslist.sig       29.86   0.14   30.00
gene.gene.statistic      25.10   0.06   25.16
gene.geneslist.statistic 23.10   0.06   23.17
paperLen                 22.97   0.05   23.01
twTStats                 20.22   0.05   20.26
twowayTable              19.57   0.04   19.63
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
actorAdjTable            37.79   3.49   59.87
gene.geneslist.sig       38.33   0.10   38.44
paperLen                 29.17   0.03   29.20
gene.geneslist.statistic 28.81   0.10   28.91
gene.gene.statistic      27.88   0.07   27.94
twTStats                 27.69   0.05   27.74
twowayTable              27.64   0.04   27.69
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/CoCiteStats.Rcheck/00check.log'
for details.


CoCiteStats.Rcheck/00install.out:


install for i386

* installing *source* package 'CoCiteStats' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'CoCiteStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoCiteStats' as CoCiteStats_1.44.0.zip
* DONE (CoCiteStats)

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

nameusersystemelapsed
actorAdjTable35.84 3.4042.70
gene.gene.statistic25.10 0.0625.16
gene.geneslist.sig29.86 0.1430.00
gene.geneslist.statistic23.10 0.0623.17
paperLen22.97 0.0523.01
twTStats20.22 0.0520.26
twowayTable19.57 0.0419.63

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

nameusersystemelapsed
actorAdjTable37.79 3.4959.87
gene.gene.statistic27.88 0.0727.94
gene.geneslist.sig38.33 0.1038.44
gene.geneslist.statistic28.81 0.1028.91
paperLen29.17 0.0329.20
twTStats27.69 0.0527.74
twowayTable27.64 0.0427.69