bumphunter 1.4.2
Rafael A. Irizarry
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/bumphunter | | Last Changed Rev: 90669 / Revision: 95116 | | Last Changed Date: 2014-05-23 10:25:54 -0700 (Fri, 23 May 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bumphunter_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/bumphunter.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.4.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘IRanges’ ‘GenomicRanges’ ‘foreach’ ‘iterators’ ‘parallel’ ‘locfit’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘bumphunter’ can be installed ... [22s/24s] WARNING
Found the following significant warnings:
Warning: bad markup (extra space?) at bumphunter.Rd:73:20
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/bumphunter.Rcheck/00_pkg_src/bumphunter/man/bumphunter.Rd:76: unexpected UNKNOWN '\item'
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/bumphunter.Rcheck/00_pkg_src/bumphunter/man/bumphunter.Rd:76: All text must be in a section
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/bumphunter.Rcheck/00_pkg_src/bumphunter/man/bumphunter.Rd:77: All text must be in a section
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/bumphunter.Rcheck/00_pkg_src/bumphunter/man/bumphunter.Rd:78: All text must be in a section
Warning: /Users/biocbuild/bbs-2.14-bioc/meat/bumphunter.Rcheck/00_pkg_src/bumphunter/man/bumphunter.Rd:81: All text must be in a section
See ‘/Users/biocbuild/bbs-2.14-bioc/meat/bumphunter.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocGenerics’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
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:
‘greaterOrEqual’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
prepare_Rd: bad markup (extra space?) at bumphunter.Rd:73:20
prepare_Rd: bumphunter.Rd:76: unexpected UNKNOWN '\item'
prepare_Rd: bumphunter.Rd:76: All text must be in a section
prepare_Rd: bumphunter.Rd:77: All text must be in a section
prepare_Rd: bumphunter.Rd:78: All text must be in a section
prepare_Rd: bumphunter.Rd:81: All text must be in a section
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'bumphunter':
\S4method{bumphunter}{matrix}
Code: function(object, design, chr = NULL, pos, cluster = NULL, coef
= 2, cutoff = NULL, pickCutoff = FALSE, pickCutoffQ =
0.99, maxGap = 500, smooth = FALSE, smoothFunction =
locfitByCluster, useWeights = FALSE, B =
ncol(permutations), permutations = NULL, verbose =
TRUE, ...)
Docs: function(object, design, chr = NULL, pos, cluster = NULL, coef
= 2, cutoff = NULL, pickCutoff = FALSE, pickCutoffQ =
0.99, maxGap = 500, smooth = FALSE, smoothFunction =
locfitByCluster, useWeights = FALSE, B = 100, verbose
= TRUE, ...)
Argument names in code not in docs:
permutations
Mismatches in argument names:
Position: 15 Code: permutations Docs: verbose
Position: 16 Code: verbose Docs: ...
Mismatches in argument default values:
Name: 'B' Code: ncol(permutations) Docs: 100
bumphunterEngine
Code: function(mat, design, chr = NULL, pos, cluster = NULL, coef =
2, cutoff = NULL, pickCutoff = FALSE, pickCutoffQ =
0.99, maxGap = 500, smooth = FALSE, smoothFunction =
locfitByCluster, useWeights = FALSE, B =
ncol(permutations), permutations = NULL, verbose =
TRUE, ...)
Docs: function(mat, design, chr = NULL, pos, cluster = NULL, coef =
2, cutoff = NULL, pickCutoff = FALSE, pickCutoffQ =
0.99, maxGap = 500, smooth = FALSE, smoothFunction =
locfitByCluster, useWeights = FALSE, B = 100, verbose
= TRUE, ...)
Argument names in code not in docs:
permutations
Mismatches in argument names:
Position: 15 Code: permutations Docs: verbose
Position: 16 Code: verbose Docs: ...
Mismatches in argument default values:
Name: 'B' Code: ncol(permutations) Docs: 100
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'bumphunter'
‘verbose’ ‘...’
Documented arguments not in \usage in documentation object 'bumphunter':
‘permutations’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [27s/22s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
bumphunter 8.992 1.756 6.140
annotateNearest 4.756 0.143 5.026
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [32s/43s]
[32s/44s] 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
WARNING: There were 4 warnings.
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/bumphunter.Rcheck/00check.log’
for details.