pepStat 1.10.0
Gregory C Imholte
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/pepStat | | Branch: RELEASE_3_5 | | Last Commit: 3f07559 | | Last Changed Date: 2017-04-24 15:45:44 -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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pepStat_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/pepStat.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pepStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pepStat’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pepStat’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘end’, ‘start’
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
.findFDR : <anonymous>: no visible global function definition for
‘median’
.sanitize_mapping_file2: no visible global function definition for
‘read.csv’
create_db: no visible global function definition for ‘mcols<-’
create_db: no visible global function definition for ‘mcols’
getWeightedEstimator : <anonymous>: no visible global function
definition for ‘lm.fit’
getWeightedEstimator : <anonymous>: no visible global function
definition for ‘lm.wfit’
getWeightedEstimator : <anonymous> : <anonymous>: no visible global
function definition for ‘sd’
plotArrayImage: no visible global function definition for
‘dev.interactive’
plotArrayImage: no visible global function definition for
‘devAskNewPage’
plotArrayImage: no visible global function definition for ‘dev.hold’
plotArrayImage: no visible global function definition for ‘dev.flush’
plotArrayResiduals: no visible global function definition for
‘dev.interactive’
plotArrayResiduals: no visible global function definition for
‘devAskNewPage’
plotArrayResiduals: no visible global function definition for
‘dev.hold’
plotArrayResiduals: no visible global function definition for
‘dev.flush’
coerce,peptideSet-ExpressionSet: no visible global function definition
for ‘annotation’
end,peptideSet: no visible global function definition for ‘end’
position,peptideSet: no visible global function definition for ‘start’
position,peptideSet: no visible global function definition for ‘end’
start,peptideSet: no visible global function definition for ‘start’
write.pSet,peptideSet: no visible global function definition for
‘start’
write.pSet,peptideSet: no visible global function definition for ‘end’
write.pSet,peptideSet: no visible global function definition for
‘write.csv’
Undefined global functions or variables:
annotation dev.flush dev.hold dev.interactive devAskNewPage end
lm.fit lm.wfit mcols mcols<- median read.csv sd start write.csv
Consider adding
importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive",
"devAskNewPage")
importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd",
"start")
importFrom("utils", "read.csv", "write.csv")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeCalls 8.354 0.111 8.894
restab 5.662 0.064 5.913
slidingMean 5.631 0.068 5.897
summarizePeptides 5.398 0.057 5.643
normalizeArray 5.344 0.068 5.572
plotArray 4.935 0.066 5.242
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/pepStat.Rcheck/00check.log’
for details.
* installing *source* package ‘pepStat’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "GenomicRanges" for requests: mcols<-
No methods found in "GenomicRanges" for requests: mcols
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "GenomicRanges" for requests: mcols<-
No methods found in "GenomicRanges" for requests: mcols
* DONE (pepStat)