Xiaobei Zhao
| Snapshot Date: 2019-03-18 17:01:12 -0400 (Mon, 18 Mar 2019) |
| URL: https://git.bioconductor.org/packages/NGScopy |
| Branch: RELEASE_3_8 |
| Last Commit: 61b4b5f |
| Last Changed Date: 2019-01-04 13:41:51 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-03-19 15:23:12 -0400 (Tue, 19 Mar 2019).
| Package 1056/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| NGScopy 1.16.1 Xiaobei Zhao
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | ERROR | ERROR | skipped | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | |
| Package: NGScopy |
| Version: 1.16.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NGScopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings NGScopy_1.16.1.tar.gz |
| StartedAt: 2019-03-19 04:19:46 -0400 (Tue, 19 Mar 2019) |
| EndedAt: 2019-03-19 04:23:50 -0400 (Tue, 19 Mar 2019) |
| EllapsedTime: 243.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NGScopy.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NGScopy.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings NGScopy_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/NGScopy.Rcheck'
* using R version 3.5.2 (2018-12-20)
* 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 '1.16.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PACKAGES'
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-3.8-bioc/meat/NGScopy.Rcheck/00check.log'
for details.
NGScopy.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/NGScopy_1.16.1.tar.gz && rm -rf NGScopy.buildbin-libdir && mkdir NGScopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NGScopy.buildbin-libdir NGScopy_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL NGScopy_1.16.1.zip && rm NGScopy_1.16.1.tar.gz NGScopy_1.16.1.zip
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100 1818k 100 1818k 0 0 29.8M 0 --:--:-- --:--:-- --:--:-- 31.7M
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
In R CMD INSTALL
install for x64
* installing *source* package 'NGScopy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NGScopy' as NGScopy_1.16.1.zip
* DONE (NGScopy)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'NGScopy' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
NGScopy.Rcheck/examples_i386/NGScopy-Ex.timings
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NGScopy.Rcheck/examples_x64/NGScopy-Ex.timings
|