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BioC 3.5: CHECK report for sincell on malbec2

This page was generated on 2017-08-16 13:16:24 -0400 (Wed, 16 Aug 2017).

Package 1229/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sincell 1.8.0
Miguel Julia , Antonio Rausell
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/sincell
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sincell
Version: 1.8.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sincell_1.8.0.tar.gz
StartedAt: 2017-08-16 02:20:25 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:21:17 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 52.0 seconds
RetCode: 0
Status:  OK 
CheckDir: sincell.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings sincell_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/sincell.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sincell/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sincell’ version ‘1.8.0’
* package encoding: UTF-8
* 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 ‘sincell’ 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
* 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 ... NOTE
sc_AssociationOfCellsHierarchyWithAGeneSet: no visible global function
  definition for ‘cor’
sc_ComparissonOfGraphs: no visible global function definition for ‘cor’
sc_ComparissonOfGraphs: no visible global function definition for
  ‘plot’
sc_ComparissonOfGraphs: no visible global function definition for
  ‘hclust’
sc_DimensionalityReductionObj: no visible global function definition
  for ‘prcomp’
sc_DimensionalityReductionObj: no visible global function definition
  for ‘cmdscale’
sc_GraphBuilderObj: no visible global function definition for ‘combn’
sc_InSilicoCellsReplicatesObj: no visible binding for global variable
  ‘var’
sc_InSilicoCellsReplicatesObj : f_mclapply: no visible global function
  definition for ‘runif’
sc_InSilicoCellsReplicatesObj : expressedvar: no visible global
  function definition for ‘var’
sc_InSilicoCellsReplicatesObj : f_mclapply: no visible binding for
  global variable ‘rnorm’
sc_InSilicoCellsReplicatesObj: no visible global function definition
  for ‘quantile’
sc_InSilicoCellsReplicatesObj : f_mclapply: no visible global function
  definition for ‘rnbinom’
sc_InitializingSincellObject: no visible binding for global variable
  ‘var’
sc_StatisticalSupportByGeneSubsampling: no visible global function
  definition for ‘cor’
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates: no
  visible global function definition for ‘cor’
sc_clusterObj: no visible global function definition for ‘hclust’
sc_clusterObj: no visible global function definition for ‘cutree’
sc_distanceObj: no visible global function definition for ‘cor’
sc_marker2color: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  cmdscale colorRampPalette combn cor cutree hclust plot prcomp
  quantile rnbinom rnorm runif var
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "cor", "cutree", "hclust", "prcomp",
             "quantile", "rnbinom", "rnorm", "runif", "var")
  importFrom("utils", "combn")
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
File ‘sincell/libs/sincell.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘pseudoreplicatesbymodel.o’, ‘pseudoreplicatesbynoise.o’,
      ‘pseudoreplicatesbynoise_cv2.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘pseudoreplicatesbymodel.o’, ‘pseudoreplicatesbynoise.o’,
      ‘pseudoreplicatesbynoise_cv2.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/sincell.Rcheck/00check.log’
for details.


sincell.Rcheck/00install.out:

* installing *source* package ‘sincell’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pseudoreplicatesbymodel.cpp -o pseudoreplicatesbymodel.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pseudoreplicatesbynoise.cpp -o pseudoreplicatesbynoise.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c pseudoreplicatesbynoise_cv2.cpp -o pseudoreplicatesbynoise_cv2.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c sstalgorithm.cpp -o sstalgorithm.o
sstalgorithm.cpp: In function ‘Rcpp::NumericVector sstalgorithm(Rcpp::NumericVector, int, Rcpp::NumericMatrix)’:
sstalgorithm.cpp:28:17: warning: ‘disty’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   out[2] = disty;
                 ^
sstalgorithm.cpp:27:17: warning: ‘distx’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   out[1] = distx;
                 ^
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o sincell.so RcppExports.o pseudoreplicatesbymodel.o pseudoreplicatesbynoise.o pseudoreplicatesbynoise_cv2.o sstalgorithm.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/sincell.Rcheck/sincell/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 (sincell)

sincell.Rcheck/sincell-Ex.timings:

nameusersystemelapsed
f_distance2vector0.0000.0000.001
sc_AssociationOfCellsHierarchyWithAGeneSet0.1360.0000.132
sc_ComparissonOfGraphs0.0360.0000.038
sc_DimensionalityReductionObj0.2040.0000.203
sc_GraphBuilderObj0.0400.0000.038
sc_InSilicoCellsReplicatesObj0.0240.0200.035
sc_InitializingSincellObject0.0160.0000.018
sc_StatisticalSupportByGeneSubsampling4.3720.1121.619
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates2.1720.1480.350
sc_clusterObj0.0360.0080.043
sc_distanceObj0.0680.0000.066
sc_marker2color0.0160.0000.013