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CHECK report for LBE on tokay2

This page was generated on 2019-04-09 11:55:35 -0400 (Tue, 09 Apr 2019).

Package 849/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LBE 1.51.0
Cyril Dalmasso
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/LBE
Branch: master
Last Commit: 4b15b3f
Last Changed Date: 2018-10-30 11:54:27 -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 [ 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: LBE
Version: 1.51.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LBE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings LBE_1.51.0.tar.gz
StartedAt: 2019-04-09 03:49:23 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:49:52 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 29.2 seconds
RetCode: 0
Status:  OK  
CheckDir: LBE.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:LBE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings LBE_1.51.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/LBE.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 'LBE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LBE' version '1.51.0'
* 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 'LBE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'stats'
A package should be listed in only one of these fields.
* 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
LBE: no visible binding for global variable 'pvalues'
Undefined global functions or variables:
  pvalues
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 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/LBE.Rcheck/00check.log'
for details.



Installation output

LBE.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/LBE_1.51.0.tar.gz && rm -rf LBE.buildbin-libdir && mkdir LBE.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LBE.buildbin-libdir LBE_1.51.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL LBE_1.51.0.zip && rm LBE_1.51.0.tar.gz LBE_1.51.0.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  114k  100  114k    0     0  1912k      0 --:--:-- --:--:-- --:--:-- 2195k

install for i386

* installing *source* package 'LBE' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'LBE'
    finding HTML links ... done
    LBE-package                             html  
    LBE                                     html  
    LBEa                                    html  
    LBEplot                                 html  
    LBEsummary                              html  
    LBEwrite                                html  
    golub.pval                              html  
    hedenfalk.pval                          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 'LBE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LBE' as LBE_1.51.0.zip
* DONE (LBE)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'LBE' successfully unpacked and MD5 sums checked

Tests output


Example timings

LBE.Rcheck/examples_i386/LBE-Ex.timings

nameusersystemelapsed
LBE0.140.010.15
LBEa0.020.000.02
LBEplot0.050.020.07
LBEsummary0.060.010.08
LBEwrite0.050.100.14

LBE.Rcheck/examples_x64/LBE-Ex.timings

nameusersystemelapsed
LBE0.140.050.18
LBEa0.020.020.03
LBEplot0.070.010.08
LBEsummary0.030.060.09
LBEwrite0.090.060.15