Package: Mulcom

Version: 1.33.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Mulcom.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Mulcom_1.33.0.tar.gz

StartedAt: 2019-03-18 03:00:19 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 03:01:34 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 75.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Mulcom.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Mulcom.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Mulcom_1.33.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Mulcom.Rcheck’
* using R Under development (unstable) (2019-01-21 r75999)
* 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 ‘1.33.0’
* 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 ... WARNING
Found the following significant warnings:
    The prototype for class “MULCOM” has undefined slot(s): 'MSE_Correceted'
See ‘/home/biocbuild/bbs-3.9-bioc/meat/Mulcom.Rcheck/00install.out’ for details.
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
mulInt 5.498  0.016   5.859
* 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 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/Mulcom.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Mulcom
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Mulcom’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o Mulcom.so mulLibs.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/Mulcom/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses,  :
  The prototype for class “MULCOM” has undefined slot(s): 'MSE_Correceted'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Mulcom)

name	user	system	elapsed
MULCOM-class	0.356	0.016	0.433
MULCOM_P	0.306	0.012	0.333
mulCAND	0.924	0.020	0.981
mulCalc	0.325	0.004	0.337
mulDELTA	0.297	0.000	0.469
mulDiff	0.886	0.016	0.912
mulFSG	0.909	0.004	0.919
mulIndex	0.280	0.004	0.286
mulInt	5.498	0.016	5.859
mulOpt	4.560	0.066	4.917
mulOptPars	0.774	0.000	0.776
mulOptPlot	1.446	0.004	1.484
mulParOpt	1.358	0.024	1.461
mulPerm	0.771	0.000	0.807
mulPermC	0.358	0.016	0.393
mulScores	0.311	0.003	0.318