Thomas Lin Pedersen
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/mzID |
| Branch: RELEASE_3_8 |
| Last Commit: 8195826 |
| Last Changed Date: 2019-01-04 13:41:34 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:10 -0400 (Sat, 13 Apr 2019).
| Package 1034/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mzID 1.20.1 Thomas Lin Pedersen
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: mzID |
| Version: 1.20.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mzID.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mzID_1.20.1.tar.gz |
| StartedAt: 2019-04-13 04:06:38 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 04:08:24 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 105.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mzID.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mzID.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mzID_1.20.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/mzID.Rcheck' * using R version 3.5.3 (2019-03-11) * 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 '1.20.1' * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/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 ... 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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-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 ** 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-3.8-bioc/meat/mzID.Rcheck/00check.log' for details.
mzID.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/mzID_1.20.1.tar.gz && rm -rf mzID.buildbin-libdir && mkdir mzID.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mzID.buildbin-libdir mzID_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL mzID_1.20.1.zip && rm mzID_1.20.1.tar.gz mzID_1.20.1.zip
###
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install for i386
* installing *source* package 'mzID' ...
** 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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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-3.8-bioc/tmpdir/RtmpMfqugD/R.INSTALL6bc5a2f394/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
In R CMD INSTALL
install for x64
* installing *source* package 'mzID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzID' as mzID_1.20.1.zip
* DONE (mzID)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'mzID' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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mzID.Rcheck/tests_i386/test-all.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 FAILED: 0
>
> proc.time()
user system elapsed
0.71 0.09 0.98
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mzID.Rcheck/tests_x64/test-all.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 FAILED: 0
>
> proc.time()
user system elapsed
0.78 0.07 0.93
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mzID.Rcheck/examples_i386/mzID-Ex.timings
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mzID.Rcheck/examples_x64/mzID-Ex.timings
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