oligoClasses 1.31.1
Benilton Carvalho and Robert Scharpf
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses | | Last Changed Rev: 103675 / Revision: 107602 | | Last Changed Date: 2015-05-11 21:24:18 -0700 (Mon, 11 May 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.31.1.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.31.1.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/oligoClasses.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.31.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
'doMC' 'doMPI' 'doRedis'
* 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 'oligoClasses' can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... NOTE
Unexported object imported by a ':::' call: 'Biobase:::assayDataEnvLock'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getSequenceLengths: no visible binding for global variable 'seqlengths'
chromosome,gSetList : .local: no visible global function definition for
'chromosomeList'
coerce,CNSet-CopyNumberSet: no visible global function definition for
'totalCopynumber'
geometry,FeatureSet: no visible global function definition for 'getPD'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [160s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeFeatureGRanges 4.79 0.06 5.91
AssayData-methods 2.98 0.07 6.52
GenomeAnnotatedDataFrame-class 1.47 0.17 134.21
** running examples for arch 'x64' ... [27s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AssayData-methods 4.82 0.14 5.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'doRUnit.R' [39s]
[40s] OK
** running tests for arch 'x64' ...
Running 'doRUnit.R' [35s]
[36s] OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/oligoClasses.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'oligoClasses' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'oligoClasses'
Creating a generic function for 'close' from package 'base' in package 'oligoClasses'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'oligoClasses' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligoClasses' as oligoClasses_1.31.1.zip
* DONE (oligoClasses)