FSA - Fisheries stock assessment methods. - check results
RForge.net

FSA

About FSA
Installation
Package R docs
Related
Check results
Download/Files
GIT access

Version: 0.8.22.9000
Result: ERROR
Check time: 2018-12-09 21:57
* using log directory ''
* using R Under development (unstable) (2018-05-16 r74729)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'FSA/DESCRIPTION' ... OK
* this is package 'FSA' version '0.8.22.9000'
* package encoding: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... 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 ... NOTE
Non-standard file/directory found at top level:
'pkgdown'
* 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 line widths ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: 'alr4', 'prettyR', 'RMark', 'PMCMR', 'pgirmess', 'agricolae'
* 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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'test-all.R' [24s/26s]
ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
test_error <<- e
register_expectation(e)
e$handled <- TRUE
test_error <<- e
}, "unused argument (TC = 19)", quote(M.empirical(Linf = 19.76, Winf = 17.3, Kl = 0.571,
Kw = 0.571, TC = 19, Bl = 10, tmax = 5.5, method = c(1:4, 9)))) at testthat/test_metaM_VALIDATE.R:30
2: eval(code, test_env)

== testthat results ===========================================================
OK: 3607 SKIPPED: 0 FAILED: 2
1. Error: vbFuns() and vbStarts() fit to Kimura separated by sex match fishmethods (and Kimura) results. (@test_VonBertalanffy_VALIDATE.R#50)
2. Error: metaM() matches M.empirical() from fishmethods for Rio Formosa Seahorse (@test_metaM_VALIDATE.R#30)

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

Status: 1 ERROR, 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)