TarSeqQC 1.1.5
Gabriela Merino
| Snapshot Date: 2016-03-28 17:20:21 -0700 (Mon, 28 Mar 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TarSeqQC | | Last Changed Rev: 114697 / Revision: 115330 | | Last Changed Date: 2016-03-13 09:02:07 -0700 (Sun, 13 Mar 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 | [ TIMEOUT ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf TarSeqQC.buildbin-libdir TarSeqQC.Rcheck && mkdir TarSeqQC.buildbin-libdir TarSeqQC.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TarSeqQC.buildbin-libdir TarSeqQC_1.1.5.tar.gz >TarSeqQC.Rcheck\00install.out 2>&1 && cp TarSeqQC.Rcheck\00install.out TarSeqQC-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=TarSeqQC.buildbin-libdir --install="check:TarSeqQC-install.out" --force-multiarch --no-vignettes --timings TarSeqQC_1.1.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/TarSeqQC.Rcheck'
* using R version 3.3.0 alpha (2016-03-17 r70348)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TarSeqQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TarSeqQC' version '1.1.5'
* 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 'TarSeqQC' 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 ... NOTE
Warning: no function found corresponding to methods exports from 'TarSeqQC' for: 'plot'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** 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 ... NOTE
Warning: no function found corresponding to methods exports from 'TarSeqQC' for: 'plot'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... 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
buildFeaturePanel,TargetExperiment : <anonymous>: no visible binding
for global variable 'sd'
buildFeaturePanel,TargetExperiment : <anonymous>: no visible binding
for global variable 'median'
buildFeaturePanel,TargetExperiment : <anonymous>: no visible binding
for global variable 'IQR'
buildReport,TargetExperiment: no visible global function definition for
'plot'
ggplotColours,TargetExperiment: no visible global function definition
for 'hcl'
initialize,TargetExperiment: no visible global function definition for
'read.delim'
plot,TargetExperiment-ANY: no visible global function definition for
'head'
plot,TargetExperiment-ANY: no visible global function definition for
'tail'
plot,TargetExperiment-ANY: no visible global function definition for
'aggregate'
plotAttrExpl,TargetExperiment: no visible global function definition
for 'sd'
plotAttrExpl,TargetExperiment: no visible global function definition
for 'median'
plotAttrExpl,TargetExperiment: no visible global function definition
for 'IQR'
plotMetaDataExpl,TargetExperiment: no visible global function
definition for 'sd'
plotMetaDataExpl,TargetExperiment: no visible global function
definition for 'median'
plotMetaDataExpl,TargetExperiment: no visible global function
definition for 'IQR'
setBedFile<-,TargetExperiment-character: no visible global function
definition for 'read.delim'
summarizePanel,TargetExperiment : <anonymous>: no visible global
function definition for 'median'
summarizePanel,TargetExperiment : <anonymous>: no visible global
function definition for 'IQR'
summarizePanel,TargetExperiment : <anonymous>: no visible global
function definition for 'sd'
Undefined global functions or variables:
IQR aggregate hcl head median plot read.delim sd tail
Consider adding
importFrom("grDevices", "hcl")
importFrom("graphics", "plot")
importFrom("stats", "IQR", "aggregate", "median", "sd")
importFrom("utils", "head", "read.delim", "tail")
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 ... 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' ... [328s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pileupCounts 1.68 0.58 206.70
TargetExperiment-readFrequencies 0.46 0.06 27.28
plotInOutFeatures 0.31 0.01 31.27
TargetExperiment-summarizePanel 0.16 0.13 52.68
** running examples for arch 'x64' ... [382s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pileupCounts 1.56 0.65 239.90
TargetExperiment-readFrequencies 0.44 0.02 34.68
plotInOutFeatures 0.26 0.05 33.75
TargetExperiment-summarizePanel 0.16 0.03 58.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [18m]
[18m] OK
** running tests for arch 'x64' ...
Running 'runTests.R'
install for i386
* installing *source* package 'TarSeqQC' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'TarSeqQC'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'TarSeqQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TarSeqQC' as TarSeqQC_1.1.5.zip
* DONE (TarSeqQC)