KCsmart 2.29.0
Jorma de Ronde
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KCsmart | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf KCsmart.buildbin-libdir KCsmart.Rcheck && mkdir KCsmart.buildbin-libdir KCsmart.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KCsmart.buildbin-libdir KCsmart_2.29.0.tar.gz >KCsmart.Rcheck\00install.out 2>&1 && cp KCsmart.Rcheck\00install.out KCsmart-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=KCsmart.buildbin-libdir --install="check:KCsmart-install.out" --force-multiarch --no-vignettes --timings KCsmart_2.29.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/KCsmart.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KCsmart/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KCsmart' version '2.29.0'
* 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 'KCsmart' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to 'siggenes' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'KernSmooth' 'siggenes'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'.add2spmc' '.checkMirrorLocs' '.comparativeKcPerms'
'.comparativeKcSiggenes' '.convertCGHbase' '.findCutoffByFdr'
'.findPeaks' '.findfdrcutoff' '.getRegions' '.getSigRegions'
'.makePermutations' '.mirrorData' '.permutedSpm' '.samplePointMatrix'
'.samplePointMatrixOld' '.snr' '.spm2spmc' '.varr'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.comparativeKcSiggenes: no visible binding for global variable 'sam'
.samplePointMatrix: no visible global function definition for 'locpoly'
.samplePointMatrix: no visible global function definition for 'bkde'
getSigRegionsCompKC: no visible global function definition for
'findDelta'
Undefined global functions or variables:
bkde findDelta locpoly sam
* 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' ... [39s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
KCsmart-package 10.50 0.11 10.61
getSigRegionsCompKC 5.62 0.03 5.65
compareSpmCollection 5.09 0.07 5.17
** running examples for arch 'x64' ... [40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
KCsmart-package 11.04 0.16 11.18
compareSpmCollection 5.36 0.13 5.49
calcSpmCollection 5.19 0.09 5.28
getSigRegionsCompKC 4.95 0.06 5.01
* 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: 3 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/KCsmart.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'KCsmart' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'write.table' from package 'utils' in package 'KCsmart'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'KCsmart' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KCsmart' as KCsmart_2.29.0.zip
* DONE (KCsmart)