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CHECK report for sincell on malbec1

This page was generated on 2021-05-06 12:29:11 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the sincell package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1722/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sincell 1.22.0  (landing page)
Miguel Julia , Antonio Rausell
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/sincell
Branch: RELEASE_3_12
Last Commit: d286cd9
Last Changed Date: 2020-10-27 11:02:22 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: sincell
Version: 1.22.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:sincell.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings sincell_1.22.0.tar.gz
StartedAt: 2021-05-06 06:06:23 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:07:25 -0400 (Thu, 06 May 2021)
EllapsedTime: 62.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sincell.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:sincell.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings sincell_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/sincell.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.22.0’
* 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 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
  ‘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 prcomp quantile
  rnbinom rnorm runif var
Consider adding
  importFrom("grDevices", "colorRampPalette")
  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
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.12-bioc/R/library/sincell/libs/sincell.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
sc_StatisticalSupportByGeneSubsampling 6.64  0.408   1.822
* 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-3.12-bioc/meat/sincell.Rcheck/00check.log’
for details.



Installation output

sincell.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL sincell
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘sincell’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pseudoreplicatesbymodel.cpp -o pseudoreplicatesbymodel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pseudoreplicatesbynoise.cpp -o pseudoreplicatesbynoise.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pseudoreplicatesbynoise_cv2.cpp -o pseudoreplicatesbynoise_cv2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-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:28:10: warning: ‘disty’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   out[2] = disty;
sstalgorithm.cpp:27:10: warning: ‘distx’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   out[1] = distx;
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-sincell/00new/sincell/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sincell)

Tests output


Example timings

sincell.Rcheck/sincell-Ex.timings

nameusersystemelapsed
f_distance2vector0.0000.0000.001
sc_AssociationOfCellsHierarchyWithAGeneSet0.0280.0000.029
sc_ComparissonOfGraphs0.0840.0000.085
sc_DimensionalityReductionObj0.1320.0000.130
sc_GraphBuilderObj0.0160.0000.016
sc_InSilicoCellsReplicatesObj0.1240.0440.145
sc_InitializingSincellObject0.0040.0000.007
sc_StatisticalSupportByGeneSubsampling6.6400.4081.822
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates0.7440.2440.340
sc_clusterObj0.0120.0040.015
sc_distanceObj0.0160.0040.019
sc_marker2color0.0080.0000.010