manta 1.17.0
Chris Berthiaume , Adrian Marchetti
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/manta | | 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 manta.buildbin-libdir manta.Rcheck && mkdir manta.buildbin-libdir manta.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=manta.buildbin-libdir manta_1.17.0.tar.gz >manta.Rcheck\00install.out 2>&1 && cp manta.Rcheck\00install.out manta-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=manta.buildbin-libdir --install="check:manta-install.out" --force-multiarch --no-vignettes --timings manta_1.17.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/manta.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 'manta/DESCRIPTION' ... OK
* this is package 'manta' version '1.17.0'
* 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 'manta' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
doc 1.4Mb
extdata 4.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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' calls in package code:
'RSQLite' 'plotrix'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
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:
'.meta2metasum'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.as.manta: no visible binding for global variable 'samples'
.as.manta: no visible binding for global variable 'counts'
.calcTMMvar: no visible binding for global variable 'x'
.checkMetaLev: no visible binding for global variable 'meta.sum'
.normalize: no visible global function definition for 'calcNormFactors'
compbiasPlot: no visible binding for global variable 'RAy'
compbiasPlot: no visible global function definition for 'violins'
counts2manta: no visible binding for global variable 'agg'
manta: no visible global function definition for 'calcNormFactors'
manta: no visible global function definition for 'estimateCommonDisp'
nf2nr: no visible global function definition for 'calcNormFactors'
nr: no visible binding for global variable 'x'
nr: no visible global function definition for 'calcNormFactors'
outGenes: no visible binding for global variable 'PValue'
outGenes: no visible binding for global variable 'R'
pplacer2manta: no visible global function definition for 'dbDriver'
pplacer2manta: no visible global function definition for 'dbConnect'
pplacer2manta: no visible global function definition for 'dbReadTable'
pplacer2manta: no visible global function definition for 'dbDisconnect'
pplacer2manta: no visible global function definition for 'dbGetQuery'
Undefined global functions or variables:
PValue R RAy agg calcNormFactors counts dbConnect dbDisconnect
dbDriver dbGetQuery dbReadTable estimateCommonDisp meta.sum samples
violins x
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.manta':
'summary.manta'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [17s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
in2manta 10.92 0.03 10.95
** running examples for arch 'x64' ... [20s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
in2manta 13.14 0.03 13.17
* 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: 5 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/manta.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'manta' ...
** R
** 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 'manta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'manta' as manta_1.17.0.zip
* DONE (manta)