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CHECK report for normr on tokay2

This page was generated on 2018-10-17 08:42:29 -0400 (Wed, 17 Oct 2018).

Package 1001/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
normr 1.6.0
Johannes Helmuth
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/normr
Branch: RELEASE_3_7
Last Commit: 4c85e97
Last Changed Date: 2018-04-30 10:35:42 -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 [ WARNINGS ] 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: normr
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:normr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings normr_1.6.0.tar.gz
StartedAt: 2018-10-17 03:40:55 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:47:33 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 397.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: normr.Rcheck
Warnings: 1

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:normr.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings normr_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/normr.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 'normr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'normr' version '1.6.0'
* 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 'normr' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpW0qiSB/R.INSTALL1e686fda2527/normr/man/NormRCountConfig-class.Rd:73: file link 'bamProfile' in package 'bamsignals' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpW0qiSB/R.INSTALL1e686fda2527/normr/man/NormRCountConfig-class.Rd:86: file link 'bamProfile' in package 'bamsignals' does not exist and so has been treated as a topic
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/normr.Rcheck/00install.out' for details.
* 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 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 ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/normr.Rcheck/00check.log'
for details.

Installation output

normr.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/normr_1.6.0.tar.gz && rm -rf normr.buildbin-libdir && mkdir normr.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=normr.buildbin-libdir normr_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL normr_1.6.0.zip && rm normr_1.6.0.tar.gz normr_1.6.0.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 2227k  100 2227k    0     0  26.8M      0 --:--:-- --:--:-- --:--:-- 29.3M

install for i386

* installing *source* package 'normr' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.7-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++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em.cpp -o em.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c normr_init.c -o normr_init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o normr.dll tmp.def RcppExports.o em.o normr_init.o -fopenmp -D_GLIBCXX_USE_C99 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/normr.buildbin-libdir/normr/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
Creating a new generic function for 'getClasses' in package 'normr'
** help
*** installing help indices
  converting help for package 'normr'
    finding HTML links ... done
    NormRCountConfig-class                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpW0qiSB/R.INSTALL1e686fda2527/normr/man/NormRCountConfig-class.Rd:73: file link 'bamProfile' in package 'bamsignals' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpW0qiSB/R.INSTALL1e686fda2527/normr/man/NormRCountConfig-class.Rd:86: file link 'bamProfile' in package 'bamsignals' does not exist and so has been treated as a topic
    NormRFit-class                          html  
    normR-diffR                             html  
    finding level-2 HTML links ... done

    normR-enrichR                           html  
    normR-regimeR                           html  
    normR                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
In R CMD INSTALL

install for x64

* installing *source* package 'normr' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.7-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++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c em.cpp -o em.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c normr_init.c -o normr_init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o normr.dll tmp.def RcppExports.o em.o normr_init.o -fopenmp -D_GLIBCXX_USE_C99 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/normr.buildbin-libdir/normr/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
* MD5 sums
packaged installation of 'normr' as normr_1.6.0.zip
* DONE (normr)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'normr' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

normr.Rcheck/tests_i386/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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(normr)

Attaching package: 'normr'

The following object is masked from 'package:methods':

    getClasses

Warning message:
replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr' 
> 
> test_check("normr")
== testthat results  ===========================================================
OK: 439 SKIPPED: 2 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  70.93    3.12   74.06

normr.Rcheck/tests_x64/testthat.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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(normr)

Attaching package: 'normr'

The following object is masked from 'package:methods':

    getClasses

Warning message:
replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr' 
> 
> test_check("normr")
== testthat results  ===========================================================
OK: 439 SKIPPED: 2 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  60.54    2.00   62.65

Example timings

normr.Rcheck/examples_i386/normr-Ex.timings

nameusersystemelapsed
NormRCountConfig-class000
NormRFit-class0.170.030.20
normR-diffR2.110.402.99
normR-enrichR2.010.222.23
normR-regimeR1.440.131.57
normR1.690.171.85

normr.Rcheck/examples_x64/normr-Ex.timings

nameusersystemelapsed
NormRCountConfig-class000
NormRFit-class0.280.000.28
normR-diffR2.440.182.67
normR-enrichR1.520.131.64
normR-regimeR1.560.191.75
normR1.340.201.55