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CHECK report for mzID on tokay1

This page was generated on 2020-04-15 12:22:07 -0400 (Wed, 15 Apr 2020).

Package 1127/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mzID 1.24.0
Laurent Gatto
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/mzID
Branch: RELEASE_3_10
Last Commit: 25c38b7
Last Changed Date: 2019-10-29 13:08:47 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: mzID
Version: 1.24.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mzID.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings mzID_1.24.0.tar.gz
StartedAt: 2020-04-15 05:02:55 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:04:34 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 99.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: mzID.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mzID.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings mzID_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/mzID.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mzID/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzID' version '1.24.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'mzID' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDdatabase.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDevidence.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDparameters.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDpeptides.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDpsm.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/mzID.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 ... NOTE
mzID: no visible binding for global variable 'i'
Undefined global functions or variables:
  i
* 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
Examples with CPU or elapsed time > 5s
     user system elapsed
mzID 1.86   0.01    5.05
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/mzID.Rcheck/00check.log'
for details.

Installation output

mzID.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/mzID_1.24.0.tar.gz && rm -rf mzID.buildbin-libdir && mkdir mzID.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mzID.buildbin-libdir mzID_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL mzID_1.24.0.zip && rm mzID_1.24.0.tar.gz mzID_1.24.0.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  485k  100  485k    0     0  14.2M      0 --:--:-- --:--:-- --:--:-- 15.8M

install for i386

* installing *source* package 'mzID' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mzID'
    finding HTML links ... done
    flatten                                 html  
    increment                               html  
    keyFor                                  html  
    mzID-class                              html  
    mzID-getters                            html  
    mzID-package                            html  
    mzID                                    html  
    mzIDCollection-class                    html  
    mzIDCollection                          html  
    mzIDdatabase-class                      html  
    mzIDdatabase                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDdatabase.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
    mzIDevidence-class                      html  
    mzIDevidence                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDevidence.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
    mzIDparameters-class                    html  
    mzIDparameters                          html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDparameters.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
    mzIDpeptides-class                      html  
    mzIDpeptides                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDpeptides.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
    mzIDpsm-class                           html  
    mzIDpsm                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpCkIHaW/R.INSTALL13c810967b4/mzID/man/mzIDpsm.Rd:11: file link 'xmlInternalTreeParse' in package 'XML' does not exist and so has been treated as a topic
    removeDecoy                             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 'mzID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzID' as mzID_1.24.0.zip
* DONE (mzID)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'mzID' successfully unpacked and MD5 sums checked

Tests output

mzID.Rcheck/tests_i386/test-all.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> 
> test_check('mzID')
Loading required package: mzID
== testthat results  ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   1.26    0.06    1.39

mzID.Rcheck/tests_x64/test-all.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)
> 
> test_check('mzID')
Loading required package: mzID
== testthat results  ===========================================================
[ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   1.35    0.10    1.51

Example timings

mzID.Rcheck/examples_i386/mzID-Ex.timings

nameusersystemelapsed
flatten0.430.021.02
mzID1.860.015.05

mzID.Rcheck/examples_x64/mzID-Ex.timings

nameusersystemelapsed
flatten0.520.010.67
mzID2.080.004.76