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BioC 3.4: CHECK report for Mulcom on zin1

This page was generated on 2016-09-21 03:37:03 -0700 (Wed, 21 Sep 2016).

Package 790/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mulcom 1.23.0
Claudio Isella
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Mulcom
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: Mulcom
Version: 1.23.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Mulcom_1.23.0.tar.gz
StartedAt: 2016-09-20 09:42:42 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:43:33 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 51.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Mulcom.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Mulcom_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Mulcom.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mulcom/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mulcom’ version ‘1.23.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Mulcom’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
* 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
'library' or 'require' call to ‘fields’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘fields’
  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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘Mulcom/R/mulib.R’:
  .First.lib calls:
    cat("Mulcom loaded\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

mulOptPlot: no visible global function definition for ‘image’
mulOptPlot: no visible global function definition for ‘image.plot’
mulParOpt: no visible global function definition for ‘image.plot’
Undefined global functions or variables:
  image image.plot
Consider adding
  importFrom("graphics", "image")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
mulInt 5.872  0.076   5.949
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/Mulcom.Rcheck/00check.log’
for details.


Mulcom.Rcheck/00install.out:

* installing *source* package ‘Mulcom’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mulLibs.cc -o mulLibs.o
mulLibs.cc: In function ‘void Single_SimulationC(double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*)’:
mulLibs.cc:708:33: warning: statement has no effect [-Wunused-value]
                 current_cluster ;
                                 ^
mulLibs.cc: In function ‘void Complete_SimulationC(double*, int*, double*, double*, int*, int*, int*, int*, int*)’:
mulLibs.cc:1022:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                  for ( int i = 0 ; i < sss2.size() ; i++ ) {
                                      ^
mulLibs.cc:1023:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                          for ( int j = 0 ; j < harmonic_means.size() ; j++ ) {
                                              ^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o Mulcom.so mulLibs.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/Mulcom.Rcheck/Mulcom/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Mulcom)

Mulcom.Rcheck/Mulcom-Ex.timings:

nameusersystemelapsed
MULCOM-class0.3720.0080.378
MULCOM_P0.2720.0040.277
mulCAND0.8400.0000.842
mulCalc0.2800.0000.277
mulDELTA0.1840.0000.183
mulDiff0.6800.0080.690
mulFSG0.7560.0000.759
mulIndex0.1800.0040.185
mulInt5.8720.0765.949
mulOpt4.6960.0284.727
mulOptPars0.6120.0040.618
mulOptPlot1.2640.0121.272
mulParOpt1.1880.0201.210
mulPerm0.6160.0080.623
mulPermC0.1840.0000.185
mulScores0.2240.0000.225