* using log directory ‘/srv/hornik/tmp/CRAN/LoopAnalyst.Rcheck’ * using R Under development (unstable) (2024-04-05 r86348) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘LoopAnalyst/DESCRIPTION’ ... OK * this is package ‘LoopAnalyst’ version ‘1.2-7’ * checking CRAN incoming feasibility ... [4s/6s] NOTE Maintainer: ‘Alexis Dinno ’ Found the following (possibly) invalid URLs: URL: https://www.journals.uchicago.edu/doi/10.1086/367590 From: man/LoopAnalyst-package.Rd man/make.T.Rd man/make.adjoint.Rd man/make.wfm.Rd man/weighted.predictions.Rd Status: 403 Message: Forbidden * 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 ‘LoopAnalyst’ can be installed ... [2s/2s] OK * checking package directory ... OK * checking for future file timestamps ... 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... 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 ... [6s/6s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) LoopAnalyst-package.Rd:14: Lost braces 14 | Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002) \doi{10.2307/3071950}{Relevance of community structure in assessing indeterminacy of ecological predictions}. \emph{Ecology}, \bold{83(5)},1372--1385. | ^ checkRd: (-1) LoopAnalyst-package.Rd:18: Lost braces 18 | Dambacher, J. M., R. Levins and P. A. Rossignol. (2005) \doi{10.1016/j.mbs.2005.06.001}{Life expectancy change in perturbed communities: Derivation and qualitative analysis}. \emph{Mathematical Biosciences} \bold{197},1--14. | ^ checkRd: (-1) LoopAnalyst-package.Rd:20: Lost braces 20 | Levins, R. (1974) \doi{10.1111/j.1749-6632.1974.tb20562.x}{Discussion Paper: The qualitative analysis of partially specified systems}. \emph{Annals of the New York Academy of Sciences}, \bold{231(1)},123--138. | ^ checkRd: (-1) LoopAnalyst-package.Rd:22: Lost braces 22 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) cem.corr.Rd:15: Lost braces 15 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. pp 55-59. | ^ checkRd: (-1) cem.levins.Rd:11: Lost braces 11 | Levins, R. and Schultz, B. B. (1996) \doi{10.2307/5678}{Effects of density dependence, feedback and environmental sensitivity on correlations among predators, prey and plant resources: Models and practical implications}. \emph{Journal of Animal Ecology}, \bold{65(6)},802-812. | ^ checkRd: (-1) cem.levins.Rd:13: Lost braces 13 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) cm.DLR.Rd:11: Lost braces 11 | Dambacher, J. M., R. Levins and P. A. Rossignol. (2005) \doi{10.1016/j.mbs.2005.06.001}{Life expectancy change in perturbed communities: Derivation and qualitative analysis}. \emph{Mathematical Biosciences} \bold{197},1--14. | ^ checkRd: (-1) cm.dambacher.Rd:11: Lost braces 11 | Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002) \doi{10.2307/3071950}{Relevance of community structure in assessing indeterminacy of ecological predictions}. \emph{Ecology}, \bold{83(5)},1372--1385. | ^ checkRd: (-1) cm.dambacher.Rd:13: Lost braces 13 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) cm.levins.Rd:11: Lost braces 11 | Levins, R. and Schultz, B. B. (1996) \doi{10.2307/5678}{Effects of density dependence, feedback and environmental sensitivity on correlations among predators, prey and plant resources: Models and practical implications}. \emph{Journal of Animal Ecology}, \bold{65(6)},802-812. | ^ checkRd: (-1) cm.levins.Rd:13: Lost braces 13 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) enumerate.loops.Rd:20: Lost braces 20 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) enumerate.paths.Rd:21: Lost braces 21 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) feedback.Rd:20: Lost braces 20 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) graph.cem.Rd:22: Lost braces 22 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) graph.cm.Rd:20: Lost braces 20 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) make.T.Rd:22: Lost braces 22 | Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002) \doi{10.2307/3071950}{Relevance of community structure in assessing indeterminacy of ecological predictions}. \emph{Ecology}, \bold{83(5)},1372--1385. | ^ checkRd: (-1) make.adjoint.Rd:22: Lost braces 22 | Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002) \doi{10.2307/3071950}{Relevance of community structure in assessing indeterminacy of ecological predictions}. \emph{Ecology}, \bold{83(5)},1372--1385. | ^ checkRd: (-1) make.cem.Rd:20: Lost braces 20 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) make.clem.Rd:19: Lost braces 19 | Dambacher, J. M., R. Levins and P. A. Rossignol. (2005) \doi{10.1016/j.mbs.2005.06.001}{Life expectancy change in perturbed communities: Derivation and qualitative analysis}. \emph{Mathematical Biosciences} \bold{197},1--14. | ^ checkRd: (-1) make.clem.Rd:21: Lost braces 21 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) make.cm.Rd:20: Lost braces 20 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) make.wfm.Rd:24: Lost braces 24 | Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002) \doi{10.2307/3071950}{Relevance of community structure in assessing indeterminacy of ecological predictions}. \emph{Ecology}, \bold{83(5)},1372--1385. | ^ checkRd: (-1) out.cm.Rd:17: Lost braces 17 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) submatrix.Rd:11: Lost braces 11 | Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002) \doi{10.2307/3071950}{Relevance of community structure in assessing indeterminacy of ecological predictions}. \emph{Ecology}, \bold{83(5)},1372--1385. | ^ checkRd: (-1) submatrix.Rd:13: Lost braces 13 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) validate.cem.Rd:17: Lost braces 17 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) validate.cm.Rd:17: Lost braces 17 | Puccia, C. J. and Levins, R. (1986) \doi{10.4159/harvard.9780674435070.c4}{\emph{Qualitative Modeling of Complex Systems: An Introduction to Loop Analysis and Time Averaging}}. Cambridge: Harvard University Press. | ^ checkRd: (-1) weighted.predictions.Rd:20: Lost braces 20 | Dambacher, J. M. and Li, H. W. and Rossignol, P. A. (2002) \doi{10.2307/3071950}{Relevance of community structure in assessing indeterminacy of ecological predictions}. \emph{Ecology}, \bold{83(5)},1372--1385. | ^ * checking Rd metadata ... OK * checking Rd line widths ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 NOTEs