Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

CHECK report for normr on tokay2

This page was generated on 2019-04-09 12:26:49 -0400 (Tue, 09 Apr 2019).

Package 1090/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
normr 1.9.0
Johannes Helmuth
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/normr
Branch: master
Last Commit: 85001a0
Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018)
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 [ WARNINGS ] 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: normr
Version: 1.9.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:normr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings normr_1.9.0.tar.gz
StartedAt: 2019-04-09 04:35:20 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:41:43 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 382.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: normr.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:normr.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings normr_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/normr.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.9.0'
* 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-3.9-bioc/tmpdir/RtmpkNlI3d/R.INSTALL1c6874123c1/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-3.9-bioc/tmpdir/RtmpkNlI3d/R.INSTALL1c6874123c1/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-3.9-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-3.9-bioc/meat/normr.Rcheck/00check.log'
for details.

Installation output

normr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/normr_1.9.0.tar.gz && rm -rf normr.buildbin-libdir && mkdir normr.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=normr.buildbin-libdir normr_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL normr_1.9.0.zip && rm normr_1.9.0.tar.gz normr_1.9.0.zip
###
##############################################################################
##############################################################################


  % 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  26.6M      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˜1.9-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/normr.buildbin-libdir/00LOCK-normr/00new/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-3.9-bioc/tmpdir/RtmpkNlI3d/R.INSTALL1c6874123c1/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-3.9-bioc/tmpdir/RtmpkNlI3d/R.INSTALL1c6874123c1/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 from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'normr'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'normr' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -fopenmp -D_GLIBCXX_USE_C99 -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-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_1.9.0.zip
* DONE (normr)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'normr' successfully unpacked and MD5 sums checked

Tests output

normr.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(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 
  50.75    2.53   53.26

normr.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(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 
  48.81    1.75   50.62

Example timings

normr.Rcheck/examples_i386/normr-Ex.timings

nameusersystemelapsed
NormRCountConfig-class000
NormRFit-class0.150.080.25
normR-diffR2.020.433.98
normR-enrichR1.840.222.06
normR-regimeR1.690.071.75
normR2.360.262.63

normr.Rcheck/examples_x64/normr-Ex.timings

nameusersystemelapsed
NormRCountConfig-class000
NormRFit-class0.750.020.77
normR-diffR1.790.101.98
normR-enrichR1.250.191.44
normR-regimeR1.250.241.48
normR1.330.201.53