FSA - Fisheries stock assessment methods. - check results
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FSA

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Version: 0.8.12
Result: ERROR
Check time: 2017-02-05 08:27
* using log directory ''
* using R version 3.3.2 Patched (2017-02-03 r72110)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* checking for file 'FSA/DESCRIPTION' ... OK
* this is package 'FSA' version '0.8.12'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
'dunn.test' 'fishmethods' 'lmtest' 'marked' 'nlstools' 'Rcapture'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'FSA' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: 'fishmethods', 'alr3', 'doBy', 'psych', 'prettyR', 'fBasics', 'Rcapture', 'RMark', 'dunn.test', 'asbio', 'PMCMR', 'pgirmess', 'agricolae', 'lmtest', 'DescTools', 'nlstools'
* 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 examples ... ERROR
Running examples in 'FSA-Ex.R' failed
The error most likely occurred in:

> ### Name: dunnTest
> ### Title: Dunn's Kruskal-Wallis Multiple Comparisons.
> ### Aliases: dunnTest dunnTest.default dunnTest.formula print.dunnTest
>
> ### ** Examples
>
> ## pH in four ponds data from Zar (2010)
> ponds <- data.frame(pond=as.factor(rep(1:4,each=8)),
+ pH=c(7.68,7.69,7.70,7.70,7.72,7.73,7.73,7.76,
+ 7.71,7.73,7.74,7.74,7.78,7.78,7.80,7.81,
+ 7.74,7.75,7.77,7.78,7.80,7.81,7.84,NA,
+ 7.71,7.71,7.74,7.79,7.81,7.85,7.87,7.91))
> ponds <- ponds[complete.cases(ponds),]
>
> # non-formula usage (default "holm" method)
> dunnTest(ponds$pH,ponds$pond)
Error in loadNamespace(name) : there is no package called 'dunn.test'
Calls: dunnTest ... tryCatch -> tryCatchList -> tryCatchOne ->
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'test-all.R'
ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
object 'tmp1' not found
1: as.matrix(tmp2[, -1] - tmp1[, -3]) at testthat/test_AgeLengthKey_VALIDATE.R:47

Loading required package: fishmethods
Error in eval(expr, envir, enclos) : could not find function "deplet"
Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'fishmethods'
testthat results ================================================================
OK: 1872 SKIPPED: 0 FAILED: 1
1. Error: alkAgeDist() reproduces results from Table 8.4 (left) of Quinn and Deriso (1999) (@test_AgeLengthKey_VALIDATE.R#47)

Error: testthat unit tests failed
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
'/00check.log'
for details.


Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log


Build log for Windows (R 2.11.x)

* checking for file 'FSA/DESCRIPTION' ... OK
* preparing 'FSA':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
WARNING: some HTML links may not be found
* installing *source* package 'FSA' ...
** R
** inst
** preparing package for lazy loading
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object(s) are masked from 'package:utils':

object.size



##########################################
## FSAdata package by Derek H. Ogle ##
## type ?FSAdata for documentation. ##
##########################################


nlstools: diagnostic tools for nonlinear regression models
version 0.0-10

Warning: package 'plotrix' was built under R version 2.11.1
Warning: package 'quantreg' was built under R version 2.11.1
Loading required package: SparseM
Warning: package 'SparseM' was built under R version 2.11.1
Package SparseM (0.86) loaded.
To cite, see citation("SparseM")


Attaching package: 'SparseM'

The following object(s) are masked from 'package:base':

backsolve


Attaching package: 'quantreg'

The following object(s) are masked from 'package:utils':

vignette

Loading required package: plyr
Warning: package 'plyr' was built under R version 2.11.1
Loading Tcl/Tk interface ... done


##########################################
## NCStats package by Derek H. Ogle ##
## type ?NCStats for documentation. ##
##########################################

** help
*** installing help indices
** building package indices ...
** MD5 sums
** testing if installed package can be loaded


##########################################
## FSA package by Derek H. Ogle ##
## type ?FSA for documentation. ##
##########################################

packaged installation of 'FSA' as FSA_0.2-1.zip

* DONE (FSA)


Build log for Windows 64-bit (R 2.11.x)

* checking for file 'FSA/DESCRIPTION' ... OK
* preparing 'FSA':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building binary distribution
WARNING: some HTML links may not be found
* installing *source* package 'FSA' ...
** R
** inst
** preparing package for lazy loading
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object(s) are masked from 'package:utils':

object.size



##########################################
## FSAdata package by Derek H. Ogle ##
## type ?FSAdata for documentation. ##
##########################################


nlstools: diagnostic tools for nonlinear regression models
version 0.0-10

Warning: package 'plotrix' was built under R version 2.11.1
Warning: package 'quantreg' was built under R version 2.11.1
Loading required package: SparseM
Package SparseM (0.85) loaded.
To cite, see citation("SparseM")


Attaching package: 'SparseM'

The following object(s) are masked from 'package:base':

backsolve


Attaching package: 'quantreg'

The following object(s) are masked from 'package:utils':

vignette

Loading required package: plyr
Warning: package 'plyr' was built under R version 2.11.1
Loading Tcl/Tk interface ... done
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
there is no package called 'NCStats'
ERROR: lazy loading failed for package 'FSA'
* removing 'c:/tmp/Rinst19622860/FSA'
ERROR
* installation failed


Build log for Mac OS X 10.5 (R 2.16.x)

ERROR: dependencies 'FSAdata', 'nlstools', 'plotrix', 'quantreg', 'reshape', 'gtools', 'Hmisc', 'NCStats', 'TeachingDemos' are not available for package 'FSA'
* removing '/Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/FSA'

Build log for Windows 7 (R 3.0.x)

(FSA 0.4.1)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'FSA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'FSA' as FSA_0.4.1.zip
* DONE (FSA)