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CHECK report for ccfindR on tokay1

This page was generated on 2019-04-13 11:29:15 -0400 (Sat, 13 Apr 2019).

Package 209/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ccfindR 1.2.1
Jun Woo
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/ccfindR
Branch: RELEASE_3_8
Last Commit: b13e377
Last Changed Date: 2019-01-03 13:45:27 -0400 (Thu, 03 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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: ccfindR
Version: 1.2.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ccfindR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ccfindR_1.2.1.tar.gz
StartedAt: 2019-04-13 01:01:01 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:06:47 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 345.5 seconds
RetCode: 0
Status:  OK  
CheckDir: ccfindR.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:ccfindR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ccfindR_1.2.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ccfindR.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 'ccfindR/DESCRIPTION' ... OK
* this is package 'ccfindR' version '1.2.1'
* 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 'ccfindR' 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
feature_map: no visible binding for global variable 'sd'
show,scNMFSet: no visible global function definition for 'head'
Undefined global functions or variables:
  head sd
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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/ccfindR/libs/i386/ccfindR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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
factorize 8.91   0.01    8.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
factorize 8.63   0.04    8.67
* 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/ccfindR.Rcheck/00check.log'
for details.



Installation output

ccfindR.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/ccfindR_1.2.1.tar.gz && rm -rf ccfindR.buildbin-libdir && mkdir ccfindR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ccfindR.buildbin-libdir ccfindR_1.2.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ccfindR_1.2.1.zip && rm ccfindR_1.2.1.tar.gz ccfindR_1.2.1.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  326k  100  326k    0     0  5987k      0 --:--:-- --:--:-- --:--:-- 6398k

install for i386

* installing *source* package 'ccfindR' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -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:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -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:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vbnmf_update.cpp -o vbnmf_update.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ccfindR.dll tmp.def RcppExports.o vbnmf_update.o -lgsl -lgslcblas -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/ccfindR.buildbin-libdir/ccfindR/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ccfindR'
    finding HTML links ... done
    basis-scNMFSet-method                   html  
    basis-set-scNMFSet-method               html  
    basis-set                               html  
    basis                                   html  
    build_tree                              html  
    ccfindR                                 html  
    cell_map                                html  
    cluster_id                              html  
    coeff-scNMFSet-method                   html  
    coeff-set-scNMFSet-method               html  
    coeff-set                               html  
    coeff                                   html  
    colData-scNMFSet-method                 html  
    colData-set-scNMFSet-ANY-method         html  
    counts-scNMFSet-method                  html  
    counts-set-scNMFSet-method              html  
    dbasis-scNMFSet-method                  html  
    dbasis-set-scNMFSet-method              html  
    dbasis-set                              html  
    dbasis                                  html  
    dcoeff-scNMFSet-method                  html  
    dcoeff-set-scNMFSet-method              html  
    dcoeff-set                              html  
    dcoeff                                  html  
    factorize                               html  
    feature_map                             html  
    filter_cells                            html  
    filter_genes                            html  
    gene_map                                html  
    measure-scNMFSet-method                 html  
    measure-set-scNMFSet-method             html  
    measure-set                             html  
    measure                                 html  
    meta_genes                              html  
    newick                                  html  
    normalize_count                         html  
    optimal_rank                            html  
    plot_genes                              html  
    plot_tree                               html  
    finding level-2 HTML links ... done

    ranks-scNMFSet-method                   html  
    ranks-set-scNMFSet-method               html  
    ranks-set                               html  
    ranks                                   html  
    read_10x                                html  
    remove_zeros                            html  
    rename_tips                             html  
    rowData-scNMFSet-method                 html  
    rowData-set-scNMFSet-method             html  
    scNMFSet-class                          html  
    scNMFSet                                html  
    show-scNMFSet-method                    html  
    simulate_data                           html  
    simulate_whx                            html  
    subset-methods                          html  
    vb_factorize                            html  
    visualize_clusters                      html  
    write_10x                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'ccfindR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -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:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -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:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c vbnmf_update.cpp -o vbnmf_update.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ccfindR.dll tmp.def RcppExports.o vbnmf_update.o -lgsl -lgslcblas -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/ccfindR.buildbin-libdir/ccfindR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ccfindR' as ccfindR_1.2.1.zip
* DONE (ccfindR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ccfindR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

ccfindR.Rcheck/examples_i386/ccfindR-Ex.timings

nameusersystemelapsed
basis-set-scNMFSet-method0.230.060.30
basis-set0.140.110.25
basis0.090.050.14
build_tree3.750.193.94
cell_map0.450.000.45
cluster_id3.430.003.43
coeff-set-scNMFSet-method0.070.000.07
coeff-set0.080.000.08
coeff0.10.00.1
colData-scNMFSet-method0.090.000.09
colData-set-scNMFSet-ANY-method0.090.000.09
counts-scNMFSet-method0.050.000.05
counts-set-scNMFSet-method0.090.000.09
factorize8.910.018.92
feature_map0.290.000.30
filter_cells0.060.000.06
filter_genes0.110.000.11
gene_map0.30.00.3
measure-set-scNMFSet-method0.080.030.11
measure-set0.080.000.07
measure0.090.000.10
meta_genes0.270.000.26
normalize_count0.060.000.06
optimal_rank3.410.083.49
plot_genes0.060.000.06
plot_tree3.440.003.61
ranks-set-scNMFSet-method0.090.000.09
ranks-set0.080.000.08
ranks0.100.000.09
read_10x0.170.020.19
remove_zeros0.070.000.06
rename_tips3.360.003.36
rowData-scNMFSet-method0.040.000.05
scNMFSet-class0.170.000.17
scNMFSet0.050.000.05
show-scNMFSet-method0.060.000.06
simulate_data0.050.000.05
simulate_whx3.370.003.37
vb_factorize3.360.003.36
visualize_clusters0.940.030.97
write_10x0.050.000.05

ccfindR.Rcheck/examples_x64/ccfindR-Ex.timings

nameusersystemelapsed
basis-set-scNMFSet-method0.400.000.42
basis-set0.280.000.28
basis0.160.000.15
build_tree3.790.003.80
cell_map0.380.020.39
cluster_id3.030.003.03
coeff-set-scNMFSet-method0.080.000.08
coeff-set0.080.000.08
coeff0.100.000.11
colData-scNMFSet-method0.110.020.12
colData-set-scNMFSet-ANY-method0.110.000.11
counts-scNMFSet-method0.070.010.08
counts-set-scNMFSet-method0.120.020.14
factorize8.630.048.67
feature_map0.360.000.36
filter_cells0.120.000.13
filter_genes0.180.000.19
gene_map0.410.000.41
measure-set-scNMFSet-method0.160.000.15
measure-set0.170.000.18
measure0.180.000.17
meta_genes0.400.000.41
normalize_count0.140.000.14
optimal_rank3.370.003.37
plot_genes0.070.000.06
plot_tree3.280.003.28
ranks-set-scNMFSet-method0.110.000.11
ranks-set0.110.000.11
ranks0.100.000.11
read_10x0.270.000.30
remove_zeros0.080.000.08
rename_tips3.480.003.48
rowData-scNMFSet-method0.070.000.06
scNMFSet-class0.180.000.19
scNMFSet0.050.000.05
show-scNMFSet-method0.060.000.07
simulate_data0.060.000.06
simulate_whx3.330.003.33
vb_factorize2.970.002.97
visualize_clusters1.090.051.14
write_10x0.110.000.11