mzID 1.2.1
Thomas Lin Pedersen
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/mzID | | Last Changed Rev: 92522 / Revision: 95116 | | Last Changed Date: 2014-07-15 12:12:54 -0700 (Tue, 15 Jul 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf mzID.buildbin-libdir && mkdir mzID.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=mzID.buildbin-libdir mzID_1.2.1.tar.gz >mzID-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=mzID.buildbin-libdir --install="check:mzID-install.out" --force-multiarch --no-vignettes --timings mzID_1.2.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/mzID.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-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 '1.2.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'mzID' can be installed ... OK
* 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'
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated alias 'length,mzID-method':
'length-mzID-method.Rd' 'length.Rd'
Rd files with duplicated alias 'length,mzIDdatabase-method':
'length-mzIDdatabase-method.Rd' 'length.Rd'
Rd files with duplicated alias 'length,mzIDevidence-method':
'length-mzIDevidence-method.Rd' 'length.Rd'
Rd files with duplicated alias 'length,mzIDparameters-method':
'length-mzIDparameters-method.Rd' 'length.Rd'
Rd files with duplicated alias 'length,mzIDpeptides-method':
'length-mzIDpeptides-method.Rd' 'length.Rd'
Rd files with duplicated alias 'length,mzIDpsm-method':
'length-mzIDpsm-method.Rd' 'length.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'names' and siglist 'mzIDCollection'
generic 'names<-' and siglist 'mzIDCollection,character'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'Utilities':
'\S4method{names}{mzIDCollection}'
Bad \usage lines found in documentation object 'Utilities':
<unescaped bksl>S4method{names<-}{mzIDCollection}(x, value)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [6s] OK
** running examples for arch 'x64' ... [6s] 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
WARNING: There were 3 warnings.
NOTE: There was 1 note.
See
'E:/biocbld/bbs-2.14-bioc/meat/mzID.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'mzID' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'mzID' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzID' as mzID_1.2.1.zip
* DONE (mzID)