encoDnaseI 0.10.0
VJ Carey
| Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/encoDnaseI | | Last Changed Rev: 3760 / Revision: 3935 | | Last Changed Date: 2016-05-03 14:35:06 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf encoDnaseI.buildbin-libdir encoDnaseI.Rcheck && mkdir encoDnaseI.buildbin-libdir encoDnaseI.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=encoDnaseI.buildbin-libdir encoDnaseI_0.10.0.tar.gz >encoDnaseI.Rcheck\00install.out 2>&1 && cp encoDnaseI.Rcheck\00install.out encoDnaseI-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=encoDnaseI.buildbin-libdir --install="check:encoDnaseI-install.out" --force-multiarch --no-vignettes --timings encoDnaseI_0.10.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-data-experiment/meat/encoDnaseI.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'encoDnaseI/DESCRIPTION' ... OK
* this is package 'encoDnaseI' version '0.10.0'
* 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 'encoDnaseI' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 4.7Mb
* 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 'lattice' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'GGBase' 'GGtools' 'lattice' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
WRC: warning in matrix(ans, nr = 2): partial argument match of 'nr' to
'nrow'
makeHg18track: warning in matrix(dataVals, nc = 1): partial argument
match of 'nc' to 'ncol'
[,hg18track-ANY-ANY-ANY: warning in matrix(dataVals(x)[kpinds], nc =
1): partial argument match of 'nc' to 'ncol'
ALICOR: no visible binding for global variable 'rawCD4'
ALICOR: no visible global function definition for 'p.value'
WRC: no visible binding for global variable 'd19'
alicor: no visible global function definition for 'approx'
alicor: no visible global function definition for 'cor'
juxtaPlot: no visible global function definition for 'p.value'
juxtaPlot: no visible global function definition for 'xyplot'
Undefined global functions or variables:
approx cor d19 p.value rawCD4 xyplot
Consider adding
importFrom("stats", "approx", "cor")
to your NAMESPACE file.
* 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 ... NOTE
Error in .requirePackage(package) :
unable to find required package 'snpMatrix'
Calls: <Anonymous> ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted
* 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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
encoDnaseI 2.8 0 5.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
encoDnaseI 3.11 0.04 5.81
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'SNPlocs.Hsapiens.dbSNP.20090506'
* 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: 6 NOTEs
See
'E:/biocbld/bbs-3.3-data-experiment/meat/encoDnaseI.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'encoDnaseI' ...
** 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 'encoDnaseI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'encoDnaseI' as encoDnaseI_0.10.0.zip
* DONE (encoDnaseI)