Thomas Lin Pedersen
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/mzID |
| Branch: master |
| Last Commit: b99ae0c |
| Last Changed Date: 2019-01-04 13:41:32 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:10:49 -0400 (Tue, 09 Apr 2019).
| Package 1061/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| mzID 1.21.1 Thomas Lin Pedersen
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: mzID |
| Version: 1.21.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mzID.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings mzID_1.21.1.tar.gz |
| StartedAt: 2019-04-09 04:30:32 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:31:34 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 62.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mzID.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mzID.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings mzID_1.21.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/mzID.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 'mzID/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzID' version '1.21.1'
* 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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-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 2.44 0.02 7.02
** 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-3.9-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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/mzID_1.21.1.tar.gz && rm -rf mzID.buildbin-libdir && mkdir mzID.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mzID.buildbin-libdir mzID_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL mzID_1.21.1.zip && rm mzID_1.21.1.tar.gz mzID_1.21.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 489k 100 489k 0 0 4850k 0 --:--:-- --:--:-- --:--:-- 5209k
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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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-3.9-bioc/tmpdir/Rtmp2VwZ93/R.INSTALLd8864533ce2/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_1.21.1.zip
* DONE (mzID)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'mzID' successfully unpacked and MD5 sums checked
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mzID.Rcheck/tests_i386/test-all.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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
1.21 0.14 1.34
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mzID.Rcheck/tests_x64/test-all.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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
1.21 0.09 1.29
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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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