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CHECK report for sincell on tokay1

This page was generated on 2019-04-13 11:24:53 -0400 (Sat, 13 Apr 2019).

Package 1456/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sincell 1.14.1
Miguel Julia , Antonio Rausell
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/sincell
Branch: RELEASE_3_8
Last Commit: 80edf44
Last Changed Date: 2019-01-04 13:50:43 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sincell
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sincell.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sincell_1.14.1.tar.gz
StartedAt: 2019-04-13 05:35:24 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:38:05 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 161.1 seconds
RetCode: 0
Status:  OK  
CheckDir: sincell.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sincell.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings sincell_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/sincell.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sincell/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sincell' version '1.14.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 '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
* 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 ... 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
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/sincell/libs/i386/sincell.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
sc_StatisticalSupportByGeneSubsampling 16.27   0.02   16.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                        user system elapsed
sc_StatisticalSupportByGeneSubsampling 16.53   0.04   16.57
* 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-3.8-bioc/meat/sincell.Rcheck/00check.log'
for details.



Installation output

sincell.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/sincell_1.14.1.tar.gz && rm -rf sincell.buildbin-libdir && mkdir sincell.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sincell.buildbin-libdir sincell_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL sincell_1.14.1.zip && rm sincell_1.14.1.tar.gz sincell_1.14.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  543k  100  543k    0     0  12.7M      0 --:--:-- --:--:-- --:--:-- 13.9M

install for i386

* installing *source* package 'sincell' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pseudoreplicatesbymodel.cpp -o pseudoreplicatesbymodel.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pseudoreplicatesbynoise.cpp -o pseudoreplicatesbynoise.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pseudoreplicatesbynoise_cv2.cpp -o pseudoreplicatesbynoise_cv2.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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;
                 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o sincell.dll tmp.def RcppExports.o pseudoreplicatesbymodel.o pseudoreplicatesbynoise.o pseudoreplicatesbynoise_cv2.o sstalgorithm.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/sincell.buildbin-libdir/sincell/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sincell'
    finding HTML links ... done
    ExpressionMatrix                        html  
    f_distance2vector                       html  
    geneset.list                            html  
    knnalgorithm                            html  
    pseudoreplicatesbymodel                 html  
    pseudoreplicatesbynoise                 html  
    pseudoreplicatesbynoise_cv2             html  
    sc_AssociationOfCellsHierarchyWithAGeneSet
                                            html  
    sc_ComparissonOfGraphs                  html  
    sc_DimensionalityReductionObj           html  
    sc_GraphBuilderObj                      html  
    sc_InSilicoCellsReplicatesObj           html  
    sc_InitializingSincellObject            html  
    sc_StatisticalSupportByGeneSubsampling
                                            html  
    sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates
                                            html  
    sc_clusterObj                           html  
    sc_distanceObj                          html  
    sc_marker2color                         html  
    sstalgorithm                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'sincell' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pseudoreplicatesbymodel.cpp -o pseudoreplicatesbymodel.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pseudoreplicatesbynoise.cpp -o pseudoreplicatesbynoise.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pseudoreplicatesbynoise_cv2.cpp -o pseudoreplicatesbynoise_cv2.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -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;
                 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o sincell.dll tmp.def RcppExports.o pseudoreplicatesbymodel.o pseudoreplicatesbynoise.o pseudoreplicatesbynoise_cv2.o sstalgorithm.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/sincell.buildbin-libdir/sincell/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sincell' as sincell_1.14.1.zip
* DONE (sincell)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'sincell' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

sincell.Rcheck/examples_i386/sincell-Ex.timings

nameusersystemelapsed
f_distance2vector0.020.000.02
sc_AssociationOfCellsHierarchyWithAGeneSet0.030.000.03
sc_ComparissonOfGraphs0.060.000.06
sc_DimensionalityReductionObj0.190.030.22
sc_GraphBuilderObj0.030.000.03
sc_InSilicoCellsReplicatesObj0.010.000.02
sc_InitializingSincellObject0.010.000.01
sc_StatisticalSupportByGeneSubsampling16.27 0.0216.28
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates1.730.001.74
sc_clusterObj0.020.010.03
sc_distanceObj0.020.000.01
sc_marker2color0.010.000.02

sincell.Rcheck/examples_x64/sincell-Ex.timings

nameusersystemelapsed
f_distance2vector000
sc_AssociationOfCellsHierarchyWithAGeneSet0.050.000.05
sc_ComparissonOfGraphs0.080.000.10
sc_DimensionalityReductionObj0.170.030.20
sc_GraphBuilderObj0.050.000.05
sc_InSilicoCellsReplicatesObj0.030.000.03
sc_InitializingSincellObject0.020.000.01
sc_StatisticalSupportByGeneSubsampling16.53 0.0416.57
sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates1.90.01.9
sc_clusterObj0.050.000.05
sc_distanceObj0.060.000.06
sc_marker2color0.020.000.02