QDNAseq 1.2.4
Daoud Sie
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/QDNAseq | | Last Changed Rev: 98557 / Revision: 102249 | | Last Changed Date: 2015-01-21 08:24:58 -0800 (Wed, 21 Jan 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |
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### Running command:
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### rm -rf QDNAseq.buildbin-libdir QDNAseq.Rcheck && mkdir QDNAseq.buildbin-libdir QDNAseq.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=QDNAseq.buildbin-libdir QDNAseq_1.2.4.tar.gz >QDNAseq.Rcheck\00install.out 2>&1 && cp QDNAseq.Rcheck\00install.out QDNAseq-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=QDNAseq.buildbin-libdir --install="check:QDNAseq-install.out" --force-multiarch --no-vignettes --timings QDNAseq_1.2.4.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/QDNAseq.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'QDNAseq/DESCRIPTION' ... OK
* this is package 'QDNAseq' version '1.2.4'
* 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 'QDNAseq' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'Biobase:::.showAnnotatedDataFrame'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'log2adhoc' 'sqrtadhoc'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createBins: no visible global function definition for 'organism'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [84s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
callBins 21.04 0.00 21.06
frequencyPlot 20.03 0.03 20.06
normalizeSegmentedBins 10.13 0.00 10.13
segmentBins 9.36 0.02 9.37
** running examples for arch 'x64' ... [82s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
frequencyPlot 21.81 0.00 21.81
callBins 20.83 0.03 20.85
segmentBins 8.79 0.00 8.80
normalizeSegmentedBins 7.06 0.03 7.09
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'QDNAseq,reproducibility.R' [12s]
Running 'QDNAseq.R' [21s]
[33s] OK
** running tests for arch 'x64' ...
Running 'QDNAseq,reproducibility.R' [14s]
Running 'QDNAseq.R' [19s]
[33s] 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
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-3.0-bioc/meat/QDNAseq.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'QDNAseq' ...
** R
** data
** 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 'QDNAseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QDNAseq' as QDNAseq_1.2.4.zip
* DONE (QDNAseq)