metaSeq 1.16.0
Koki Tsuyuzaki
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/metaSeq | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings metaSeq_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/metaSeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaSeq’ version ‘1.16.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘metaSeq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
data 5.8Mb
* 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
* 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 objects imported by ':::' calls:
‘NOISeq:::busca’ ‘NOISeq:::n.menor’
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:
‘oneside.noiseq’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘metaSeq/R/Accelerate.NOISeq.R’:
assignInNamespace("busca", busca, ns = "NOISeq", envir = env)
assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env)
assignInNamespace("busca", busca, ns = "NOISeq", envir = env)
assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env)
File ‘metaSeq/R/Reset.Accelerate.NOISeq.R’:
assignInNamespace("busca", original.busca, ns = "NOISeq", envir = env)
assignInNamespace("n.menor", original.n.menor, ns = "NOISeq",
envir = env)
File ‘metaSeq/R/oneside.noiseq.R’:
assignInNamespace("probdeg", custom.probdeg, ns = "NOISeq", envir = env)
assignInNamespace("MD", custom.MD, ns = "NOISeq", envir = env)
assignInNamespace("probdeg", original.probdeg, ns = "NOISeq",
envir = env)
assignInNamespace("MD", original.MD, ns = "NOISeq", envir = env)
Accelerate.NOISeq: no visible global function definition for ‘data’
Accelerate.NOISeq: no visible binding for global variable
‘text.n.menor_unix’
Accelerate.NOISeq: no visible binding for global variable
‘text.busca_unix’
Accelerate.NOISeq: no visible global function definition for
‘assignInNamespace’
Accelerate.NOISeq: no visible binding for global variable ‘busca’
Accelerate.NOISeq: no visible binding for global variable ‘nmenor’
Accelerate.NOISeq: no visible binding for global variable
‘text.n.menor_win’
Accelerate.NOISeq: no visible binding for global variable
‘text.busca_win’
Reset.Accelerate.NOISeq: no visible global function definition for
‘assignInNamespace’
custom.MD: no visible global function definition for ‘combn’
custom.probdeg: no visible global function definition for ‘na.omit’
each.Fisher.ignore.test: no visible global function definition for
‘pchisq’
each.Fisher.test: no visible global function definition for ‘pchisq’
each.Stouffer.ignore.test: no visible global function definition for
‘qnorm’
each.Stouffer.ignore.test: no visible global function definition for
‘pnorm’
each.Stouffer.test: no visible global function definition for ‘qnorm’
each.Stouffer.test: no visible global function definition for ‘pnorm’
oneside.noiseq: no visible global function definition for
‘assignInNamespace’
original.MD: no visible global function definition for ‘combn’
original.probdeg: no visible global function definition for ‘na.omit’
original.probdeg: no visible binding for global variable ‘n.menor’
original.probdeg: no visible binding for global variable ‘busca’
Undefined global functions or variables:
assignInNamespace busca combn data n.menor na.omit nmenor pchisq
pnorm qnorm text.busca_unix text.busca_win text.n.menor_unix
text.n.menor_win
Consider adding
importFrom("stats", "na.omit", "pchisq", "pnorm", "qnorm")
importFrom("utils", "assignInNamespace", "combn", "data")
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’ ... NOTE
The following files should probably not be installed:
‘Fig1.jpeg’, ‘Fig2.png’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/metaSeq.Rcheck/00check.log’
for details.