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CHECK report for pepXMLTab on tokay2

This page was generated on 2018-10-17 08:39:40 -0400 (Wed, 17 Oct 2018).

Package 1079/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepXMLTab 1.14.0
Xiaojing Wang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/pepXMLTab
Branch: RELEASE_3_7
Last Commit: 6b95187
Last Changed Date: 2018-04-30 10:35:35 -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 [ 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

Summary

Package: pepXMLTab
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pepXMLTab.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings pepXMLTab_1.14.0.tar.gz
StartedAt: 2018-10-17 03:55:34 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:56:10 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 36.0 seconds
RetCode: 0
Status:  OK  
CheckDir: pepXMLTab.Rcheck
Warnings: 0

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:pepXMLTab.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings pepXMLTab_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/pepXMLTab.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 'pepXMLTab/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pepXMLTab' version '1.14.0'
* 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 'pepXMLTab' 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.
* 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 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 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/pepXMLTab.Rcheck/00check.log'
for details.

Installation output

pepXMLTab.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/pepXMLTab_1.14.0.tar.gz && rm -rf pepXMLTab.buildbin-libdir && mkdir pepXMLTab.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pepXMLTab.buildbin-libdir pepXMLTab_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL pepXMLTab_1.14.0.zip && rm pepXMLTab_1.14.0.tar.gz pepXMLTab_1.14.0.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  104k  100  104k    0     0  1946k      0 --:--:-- --:--:-- --:--:-- 2222k

install for i386

* installing *source* package 'pepXMLTab' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pepXMLTab'
    finding HTML links ... done
    PSMfilter                               html  
    pepXML2tab                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pepXMLTab' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pepXMLTab' as pepXMLTab_1.14.0.zip
* DONE (pepXMLTab)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'pepXMLTab' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

pepXMLTab.Rcheck/tests_i386/runTests.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.

> BiocGenerics:::testPackage("pepXMLTab")
No input data
No input data


RUNIT TEST PROTOCOL -- Wed Oct 17 03:56:03 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
pepXMLTab RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.21    0.10    1.32

pepXMLTab.Rcheck/tests_x64/runTests.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.

> BiocGenerics:::testPackage("pepXMLTab")
No input data
No input data


RUNIT TEST PROTOCOL -- Wed Oct 17 03:56:06 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
pepXMLTab RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   1.70    0.15    1.84

Example timings

pepXMLTab.Rcheck/examples_i386/pepXMLTab-Ex.timings

nameusersystemelapsed
PSMfilter0.490.000.63
pepXML2tab1.190.011.81

pepXMLTab.Rcheck/examples_x64/pepXMLTab-Ex.timings

nameusersystemelapsed
PSMfilter0.550.030.57
pepXML2tab1.430.031.50