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CHECK report for NGScopy on tokay2

This page was generated on 2019-03-11 11:26:44 -0400 (Mon, 11 Mar 2019).

Package 1071/1676HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NGScopy 1.17.1
Xiaobei Zhao
Snapshot Date: 2019-03-10 17:02:02 -0400 (Sun, 10 Mar 2019)
URL: https://git.bioconductor.org/packages/NGScopy
Branch: master
Last Commit: ae7ebdd
Last Changed Date: 2019-01-04 13:41:49 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.1 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: NGScopy
Version: 1.17.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NGScopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings NGScopy_1.17.1.tar.gz
StartedAt: 2019-03-11 04:52:31 -0400 (Mon, 11 Mar 2019)
EndedAt: 2019-03-11 04:54:12 -0400 (Mon, 11 Mar 2019)
EllapsedTime: 101.2 seconds
RetCode: 0
Status:  OK  
CheckDir: NGScopy.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:NGScopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings NGScopy_1.17.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/NGScopy.Rcheck'
* using R Under development (unstable) (2019-01-10 r75962)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NGScopy/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NGScopy' version '1.17.1'
* 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 'NGScopy' 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
.count_starts: no visible global function definition for 'median'
.count_starts: no visible global function definition for 'sd'
.help_segmtype: no visible global function definition for 'help'
.make_windows : .unit: no visible global function definition for
  'median'
.make_windows : .unit: no visible global function definition for 'sd'
.plot_out: no visible global function definition for 'pdf'
.plot_out: no visible global function definition for 'dev.off'
.unit_plot_out: no visible global function definition for 'par'
read_regions: no visible global function definition for 'read.table'
Undefined global functions or variables:
  dev.off help median par pdf read.table sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
  importFrom("utils", "help", "read.table")
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 files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'ngscopy-case1b-cmdline.out'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/NGScopy.Rcheck/00check.log'
for details.



Installation output

NGScopy.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/NGScopy_1.17.1.tar.gz && rm -rf NGScopy.buildbin-libdir && mkdir NGScopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NGScopy.buildbin-libdir NGScopy_1.17.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL NGScopy_1.17.1.zip && rm NGScopy_1.17.1.tar.gz NGScopy_1.17.1.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 1822k  100 1822k    0     0  10.6M      0 --:--:-- --:--:-- --:--:-- 11.1M

install for i386

* installing *source* package 'NGScopy' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'NGScopy'
    finding HTML links ... done
    NGScopy-class                           html  
    NGScopy-package                         html  
    df.to.gr                                html  
    help_segmtype                           html  
    ngscopy_cmdline_example                 html  
    ngscopy_unittest                        html  
    parse_segmtype                          html  
    read_regions                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'NGScopy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NGScopy' as NGScopy_1.17.1.zip
* DONE (NGScopy)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'NGScopy' successfully unpacked and MD5 sums checked

Tests output


Example timings

NGScopy.Rcheck/examples_i386/NGScopy-Ex.timings

nameusersystemelapsed
NGScopy-class0.780.032.82
df.to.gr000
help_segmtype000
ngscopy_cmdline_example0.000.010.01
ngscopy_unittest000
parse_segmtype000
read_regions0.020.000.01

NGScopy.Rcheck/examples_x64/NGScopy-Ex.timings

nameusersystemelapsed
NGScopy-class0.690.030.98
df.to.gr000
help_segmtype000
ngscopy_cmdline_example0.010.000.02
ngscopy_unittest000
parse_segmtype0.000.010.01
read_regions000