Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for apComplex on tokay1

This page was generated on 2017-04-15 16:14:38 -0400 (Sat, 15 Apr 2017).

Package 57/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
apComplex 2.40.0
Denise Scholtens
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/apComplex
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: apComplex
Version: 2.40.0
Command: rm -rf apComplex.buildbin-libdir apComplex.Rcheck && mkdir apComplex.buildbin-libdir apComplex.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=apComplex.buildbin-libdir apComplex_2.40.0.tar.gz >apComplex.Rcheck\00install.out 2>&1 && cp apComplex.Rcheck\00install.out apComplex-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=apComplex.buildbin-libdir --install="check:apComplex-install.out" --force-multiarch --no-vignettes --timings apComplex_2.40.0.tar.gz
StartedAt: 2017-04-14 20:59:17 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:01:13 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 116.2 seconds
RetCode: 0
Status:  OK  
CheckDir: apComplex.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf apComplex.buildbin-libdir apComplex.Rcheck && mkdir apComplex.buildbin-libdir apComplex.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=apComplex.buildbin-libdir apComplex_2.40.0.tar.gz >apComplex.Rcheck\00install.out 2>&1 && cp apComplex.Rcheck\00install.out apComplex-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=apComplex.buildbin-libdir --install="check:apComplex-install.out" --force-multiarch --no-vignettes --timings apComplex_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/apComplex.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'apComplex/DESCRIPTION' ... OK
* this is package 'apComplex' version '2.40.0'
* 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 'apComplex' 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'RBGL' 'graph'
  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
plotComplex: warning in mget(complexMembers, env = org.Sc.sgdGENENAME,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
bhmaxSubgraph: no visible global function definition for 'as'
bhmaxSubgraph: no visible global function definition for 'ugraph'
bhmaxSubgraph: no visible global function definition for 'maxClique'
plotComplex: no visible global function definition for 'subGraph'
plotComplex: no visible global function definition for
  'removeSelfLoops'
plotComplex: no visible global function definition for 'edgeNames'
plotComplex: no visible global function definition for 'numEdges'
plotComplex: no visible global function definition for 'degree'
Undefined global functions or variables:
  as degree edgeNames maxClique numEdges removeSelfLoops subGraph
  ugraph
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
** running examples for arch 'x64' ... OK
* 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-3.4-bioc/meat/apComplex.Rcheck/00check.log'
for details.


apComplex.Rcheck/00install.out:


install for i386

* installing *source* package 'apComplex' ...
** 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 'apComplex' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'apComplex' as apComplex_2.40.0.zip
* DONE (apComplex)

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

nameusersystemelapsed
FilteredEstimates0.050.020.06
HMSPCI0.170.000.17
Krogan000
LCjoin0.150.020.23
MBMEcHMSPCI0.020.000.02
MBMEcKrogan000
MBMEcTAP0.020.000.01
TAP0.010.000.03
apEX0.000.010.02
bhmaxSubgraph0.110.000.11
findComplexes0.020.000.02
gavinBP20060.110.030.14
kroganBPMat20060.290.050.34
mergeComplexes0.130.020.14
plotComplex0.040.000.13
sortComplexes0.020.000.01
yNameTAP0.030.000.03
yTAP000

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

nameusersystemelapsed
FilteredEstimates0.050.020.07
HMSPCI0.20.00.2
Krogan000
LCjoin0.250.021.69
MBMEcHMSPCI000
MBMEcKrogan000
MBMEcTAP0.010.000.02
TAP0.030.000.03
apEX000
bhmaxSubgraph0.160.010.17
findComplexes0.160.000.16
gavinBP20060.090.030.12
kroganBPMat20060.220.100.31
mergeComplexes0.020.030.05
plotComplex0.040.010.31
sortComplexes0.020.020.04
yNameTAP0.010.000.01
yTAP0.020.000.02