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CHECK report for destiny on tokay2

This page was generated on 2019-10-16 12:33:44 -0400 (Wed, 16 Oct 2019).

Package 426/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
destiny 2.14.0
Philipp Angerer
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/destiny
Branch: RELEASE_3_9
Last Commit: bd347a8
Last Changed Date: 2019-05-02 11:53:56 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: destiny
Version: 2.14.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:destiny.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings destiny_2.14.0.tar.gz
StartedAt: 2019-10-16 03:13:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:19:51 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 393.0 seconds
RetCode: 0
Status:  OK  
CheckDir: destiny.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:destiny.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings destiny_2.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/destiny.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'destiny/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'destiny' version '2.14.0'
* 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 whether package 'destiny' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'SingleCellExperiment'
A package should be listed in only one of these fields.
'LinkingTo' for 'grDevices' is unused as it has no 'include' directory
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.DPT plot.DiffusionMap
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.DPT':
  'plot.DPT'

S3 methods shown with full name in documentation object 'plot.DiffusionMap':
  'plot.DiffusionMap'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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-3.9-bioc/R/library/destiny/libs/i386/destiny.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/destiny/libs/x64/destiny.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
destiny                 27.86   0.23   28.43
Gene-Relevance-plotting  6.87   0.35    7.56
DiffusionMap-class       4.92   0.32    5.23
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
destiny                 10.48   0.11   10.59
Gene-Relevance-plotting  5.15   0.26    5.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/destiny.Rcheck/00check.log'
for details.



Installation output

destiny.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/destiny_2.14.0.tar.gz && rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=destiny.buildbin-libdir destiny_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL destiny_2.14.0.zip && rm destiny_2.14.0.tar.gz destiny_2.14.0.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 1717k  100 1717k    0     0  6347k      0 --:--:-- --:--:-- --:--:-- 6507k

install for i386

* installing *source* package 'destiny' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/grDevices/include"   -I"C:/extsoft/include"  -ggdb   -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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/grDevices/include"   -I"C:/extsoft/include"  -ggdb   -O2 -Wall  -mtune=generic -c censoring.cpp -o censoring.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/grDevices/include"   -I"C:/extsoft/include"  -ggdb   -O2 -Wall  -mtune=generic -c knn.cpp -o knn.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/grDevices/include"   -I"C:/extsoft/include"  -ggdb   -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o knn.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/destiny.buildbin-libdir/00LOCK-destiny/00new/destiny/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'destiny'
    finding HTML links ... done
    DPT-matrix-methods                      html  
    DPT-methods                             html  
    DPT                                     html  
    DiffusionMap-accessors                  html  
    DiffusionMap-class                      html  
    DiffusionMap-methods                    html  
    ExpressionSet-helpers                   html  
    Gene-Relevance-methods                  html  
    Gene-Relevance-plotting                 html  
    Gene-Relevance                          html  
    Sigmas-class                            html  
    coercions                               html  
    colorlegend                             html  
    cube_helix                              html  
    destiny-deprecated                      html  
    destiny-generics                        html  
    destiny                                 html  
    dm_predict                              html  
    eig_decomp                              html  
    extractions                             html  
    find_dm_k                               html  
    find_sigmas                             html  
    find_tips                               html  
    guo                                     html  
    knn                                     html  
    l_which                                 html  
    plot.DPT                                html  
    plot.DiffusionMap                       html  
    plot.Sigmas                             html  
    projection_dist                         html  
    random_root                             html  
    updateObject-method                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/grDevices/include"   -I"C:/extsoft/include"  -ggdb   -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-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/grDevices/include"   -I"C:/extsoft/include"  -ggdb   -O2 -Wall  -mtune=generic -c censoring.cpp -o censoring.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/grDevices/include"   -I"C:/extsoft/include"  -ggdb   -O2 -Wall  -mtune=generic -c knn.cpp -o knn.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/grDevices/include"   -I"C:/extsoft/include"  -ggdb   -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o knn.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/destiny.buildbin-libdir/destiny/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'destiny' as destiny_2.14.0.zip
* DONE (destiny)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'destiny' successfully unpacked and MD5 sums checked

Tests output

destiny.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(destiny)
> 
> test_check('destiny')
== testthat results  ===========================================================
[ OK: 51 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  10.71    1.01   11.70 

destiny.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(destiny)
> 
> test_check('destiny')
== testthat results  ===========================================================
[ OK: 51 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.73    0.68   15.46 

Example timings

destiny.Rcheck/examples_i386/destiny-Ex.timings

nameusersystemelapsed
DPT-methods2.920.383.31
DPT1.790.151.95
DiffusionMap-accessors1.000.171.17
DiffusionMap-class4.920.325.23
DiffusionMap-methods1.080.181.27
ExpressionSet-helpers0.140.000.14
Gene-Relevance-methods2.740.333.06
Gene-Relevance-plotting6.870.357.56
Gene-Relevance2.550.122.68
Sigmas-class0.250.020.27
coercions1.070.091.15
colorlegend0.010.000.02
cube_helix0.020.000.02
destiny-deprecated000
destiny-generics1.070.141.21
destiny27.86 0.2328.43
dm_predict0.660.070.71
eig_decomp000
extractions1.330.121.46
find_dm_k000
find_sigmas0.950.111.06
find_tips1.240.161.39
l_which000
plot.DPT2.290.032.33
plot.DiffusionMap1.070.221.28
plot.Sigmas0.260.030.30
projection_dist0.450.010.47
random_root1.380.161.53

destiny.Rcheck/examples_x64/destiny-Ex.timings

nameusersystemelapsed
DPT-methods2.170.232.41
DPT1.890.051.93
DiffusionMap-accessors1.610.201.82
DiffusionMap-class4.170.184.34
DiffusionMap-methods0.770.120.89
ExpressionSet-helpers0.070.000.08
Gene-Relevance-methods1.630.161.78
Gene-Relevance-plotting5.150.265.42
Gene-Relevance2.420.032.45
Sigmas-class0.190.020.20
coercions1.140.051.19
colorlegend0.020.000.02
cube_helix0.010.000.01
destiny-deprecated000
destiny-generics1.440.011.46
destiny10.48 0.1110.59
dm_predict0.570.050.61
eig_decomp000
extractions1.170.041.22
find_dm_k000
find_sigmas0.910.040.94
find_tips1.290.041.34
l_which000
plot.DPT2.160.082.23
plot.DiffusionMap0.810.110.93
plot.Sigmas0.250.000.25
projection_dist0.360.020.37
random_root0.730.070.81