LymphoSeq 1.3.0
David Coffey
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq | | Last Changed Rev: 125570 / Revision: 127142 | | Last Changed Date: 2017-01-02 19:58:34 -0500 (Mon, 02 Jan 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | ERROR | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ ERROR ] | 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 LymphoSeq_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/LymphoSeq.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LymphoSeq/DESCRIPTION’ ... OK
* this is package ‘LymphoSeq’ version ‘1.3.0’
* 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 ‘LymphoSeq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
extdata 5.5Mb
* checking package 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
phyloTree: no visible binding for global variable ‘dominant’
phyloTree: no visible binding for global variable ‘count’
Undefined global functions or variables:
count dominant
* checking Rd files ... OK
* 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 'phyloTree':
phyloTree
Code: function(list, sample, type = "nucleotide", layout =
"rectangular", label = TRUE)
Docs: function(list, sample, type = "nucleotide", layout =
"rectangular")
Argument names in code not in docs:
label
Codoc mismatches from documentation object 'readImmunoSeq':
readImmunoSeq
Code: function(path, columns = c("aminoAcid", "nucleotide", "count",
"count (templates)", "count (reads)", "count
(templates/reads)", "frequencyCount", "frequencyCount
(%)", "estimatedNumberGenomes", "vFamilyName",
"dFamilyName", "jFamilyName", "vGeneName",
"dGeneName", "jGeneName"), recursive = FALSE)
Docs: function(path, columns = c("aminoAcid", "nucleotide", "count",
"count (templates)", "count (reads)",
"frequencyCount", "frequencyCount (%)",
"estimatedNumberGenomes", "vFamilyName",
"dFamilyName", "jFamilyName", "vGeneName",
"dGeneName", "jGeneName"), recursive = FALSE)
Mismatches in argument default values:
Name: 'columns'
Code: c("aminoAcid", "nucleotide", "count", "count (templates)", "count (reads)",
"count (templates/reads)", "frequencyCount", "frequencyCount (%)",
"estimatedNumberGenomes", "vFamilyName", "dFamilyName", "jFamilyName",
"vGeneName", "dGeneName", "jGeneName")
Docs: c("aminoAcid", "nucleotide", "count", "count (templates)", "count (reads)",
"frequencyCount", "frequencyCount (%)", "estimatedNumberGenomes",
"vFamilyName", "dFamilyName", "jFamilyName", "vGeneName",
"dGeneName", "jGeneName")
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘LymphoSeq.Rmd’
* checking examples ... ERROR
Running examples in ‘LymphoSeq-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alignSeq
> ### Title: Align mutliple sequences
> ### Aliases: alignSeq
>
> ### ** Examples
>
> file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")
>
> file.list <- readImmunoSeq(path = file.path)
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>
> productive.nt <- productiveSeq(file.list = file.list, aggregate = "nucleotide")
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>
> alignSeq(list = productive.nt, sample = "TCRB_Day1320_CD8_CMV", type = "nucleotide",
+ method = "ClustalW")
Error in if (nrow(file) > 150) { : argument is of length zero
Calls: alignSeq
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/LymphoSeq.Rcheck/00check.log’
for details.