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CHECK report for ccfindR on tokay2

This page was generated on 2018-10-17 08:45:47 -0400 (Wed, 17 Oct 2018).

Package 196/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ccfindR 1.0.0
Jun Woo
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ccfindR
Branch: RELEASE_3_7
Last Commit: b9f8f06
Last Changed Date: 2018-04-30 10:35:51 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ccfindR
Version: 1.0.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ccfindR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ccfindR_1.0.0.tar.gz
StartedAt: 2018-10-17 00:57:27 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:03:33 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 365.5 seconds
RetCode: 0
Status:  OK  
CheckDir: ccfindR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ccfindR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ccfindR_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ccfindR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.0.0'
* 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 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot_tree    11.33   0.10   11.44
cluster_id   10.27   0.00   10.27
vb_factorize  9.69   0.00    9.69
build_tree    9.53   0.08    9.61
simulate_whx  9.51   0.00    9.51
rename_tips   9.29   0.03    9.33
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
build_tree              17.01   0.00   17.02
cluster_id              13.77   0.00   13.76
plot_tree               11.07   0.05   11.12
rename_tips              9.61   0.00    9.61
simulate_whx             9.61   0.00    9.61
vb_factorize             8.86   0.00    8.86
factorize                5.27   0.04    5.31
colData-scNMFSet-method  0.19   0.02   11.75
* 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: OK


Installation output

ccfindR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ccfindR_1.0.0.tar.gz && rm -rf ccfindR.buildbin-libdir && mkdir ccfindR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ccfindR.buildbin-libdir ccfindR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ccfindR_1.0.0.zip && rm ccfindR_1.0.0.tar.gz ccfindR_1.0.0.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  320k  100  320k    0     0  5054k      0 --:--:-- --:--:-- --:--:-- 5715k

install for i386

* installing *source* package 'ccfindR' ...
** 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  
    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  
    factorize                               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  
    normalize_count                         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' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ccfindR' as ccfindR_1.0.0.zip
* DONE (ccfindR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-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-method0.290.080.38
basis-set0.210.150.36
basis0.360.030.39
build_tree9.530.089.61
cell_map1.120.001.12
cluster_id10.27 0.0010.27
coeff-set-scNMFSet-method0.290.000.30
coeff-set0.290.000.28
coeff0.610.000.61
colData-scNMFSet-method0.150.000.15
colData-set-scNMFSet-ANY-method0.140.000.14
counts-scNMFSet-method0.080.000.08
counts-set-scNMFSet-method0.140.000.14
factorize3.470.043.52
filter_cells0.070.000.08
filter_genes0.110.000.11
gene_map1.160.001.15
measure-set-scNMFSet-method0.160.000.16
measure-set0.170.000.17
measure0.360.000.36
meta_genes1.500.111.61
normalize_count0.070.000.08
plot_genes0.070.000.06
plot_tree11.33 0.1011.44
ranks-set-scNMFSet-method0.370.000.37
ranks-set0.260.010.28
ranks0.360.000.36
read_10x0.170.000.17
remove_zeros0.100.000.09
rename_tips9.290.039.33
rowData-scNMFSet-method0.050.000.05
scNMFSet-class0.140.040.17
scNMFSet0.050.000.05
show-scNMFSet-method0.040.000.04
simulate_data0.070.000.07
simulate_whx9.510.009.51
vb_factorize9.690.009.69
visualize_clusters2.410.002.41
write_10x0.090.000.09

ccfindR.Rcheck/examples_x64/ccfindR-Ex.timings

nameusersystemelapsed
basis-set-scNMFSet-method0.480.010.50
basis-set0.350.050.39
basis0.600.020.61
build_tree17.01 0.0017.02
cell_map1.750.011.77
cluster_id13.77 0.0013.76
coeff-set-scNMFSet-method0.170.000.18
coeff-set0.170.000.17
coeff0.580.000.57
colData-scNMFSet-method 0.19 0.0211.75
colData-set-scNMFSet-ANY-method0.140.030.17
counts-scNMFSet-method0.090.000.09
counts-set-scNMFSet-method0.190.000.19
factorize5.270.045.31
filter_cells0.170.000.17
filter_genes0.200.000.21
gene_map2.190.002.18
measure-set-scNMFSet-method0.360.000.36
measure-set0.250.000.25
measure0.480.000.49
meta_genes2.030.002.03
normalize_count0.180.000.17
plot_genes0.110.000.11
plot_tree11.07 0.0511.12
ranks-set-scNMFSet-method0.270.000.27
ranks-set0.260.000.27
ranks0.380.000.37
read_10x0.200.020.22
remove_zeros0.100.000.09
rename_tips9.610.009.61
rowData-scNMFSet-method0.060.000.06
scNMFSet-class0.220.000.22
scNMFSet0.060.000.07
show-scNMFSet-method0.060.000.06
simulate_data0.060.000.06
simulate_whx9.610.009.61
vb_factorize8.860.008.86
visualize_clusters2.100.002.09
write_10x0.060.000.07