From 7891f4d15045da2109fcc273b85ac264195ce8c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Kirill=20M=C3=BCller?= Date: Sat, 9 Dec 2023 12:48:55 +0100 Subject: [PATCH] Results with all problems --- revdep/README.md | 24 ++++ revdep/problems.md | 318 +++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 342 insertions(+) diff --git a/revdep/README.md b/revdep/README.md index ea2d2ffa1c..cb6b4b4284 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -7,3 +7,27 @@ |[influential](problems.md#influential)|2.2.8 | |__+2__ | | |[statGraph](problems.md#statgraph)|0.5.0 |__+1__ | | | +## All (19) + +|package |version |error |warning |note | +|:-----------------|:-------|:------|:-------|:----| +|[causaleffect](problems.md#causaleffect)|1.3.15 | |1 | | +|centiserve |1.0.0 | | | | +|cfid |0.1.7 | | | | +|[CINNA](problems.md#cinna)|1.2.2 | | |1 | +|[dosearch](problems.md#dosearch)|1.0.8 | | |2 | +|fanovaGraph |1.5 | | | | +|[ggnetwork](problems.md#ggnetwork)|0.5.12 | | |1 | +|[inferCSN](problems.md#infercsn)|0.99.8 | | |1 | +|[influential](problems.md#influential)|2.2.8 | |__+2__ | | +|intergraph |2.0-3 | | | | +|[markovchain](problems.md#markovchain)|0.9.5 |1 | |3 | +|nosoi |1.1.0 | | | | +|[pcalg](problems.md#pcalg)|2.7-9 | | |3 | +|[phyloseqGraphTest](problems.md#phyloseqgraphtest)|0.1.0 | | |2 | +|rgraph6 |2.0-2 | | | | +|riverconn |0.3.28 | | | | +|[shazam](problems.md#shazam)|1.2.0 | |1 | | +|[statGraph](problems.md#statgraph)|0.5.0 |__+1__ | | | +|TreeDimensionTest |0.0.2 | | | | + diff --git a/revdep/problems.md b/revdep/problems.md index 76ddadaff4..23c94a5da8 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,3 +1,141 @@ +# causaleffect + +
+ +* Version: 1.3.15 +* GitHub: https://github.com/santikka/causaleffect +* Source code: https://github.com/cran/causaleffect +* Date/Publication: 2022-07-14 09:10:05 UTC +* Number of recursive dependencies: 17 + +Run `revdepcheck::cloud_details(, "causaleffect")` for more info + +
+ +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘causaleffect.ltx’ using tex + Error: processing vignette 'causaleffect.ltx' failed with diagnostics: + Running 'texi2dvi' on 'causaleffect.ltx' failed. + LaTeX errors: + ! LaTeX Error: File `thumbpdf.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + + ... + l.16 \usepackage + {csquotes}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘simplification.ltx’ + + SUMMARY: processing the following files failed: + ‘causaleffect.ltx’ ‘simplification.ltx’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# CINNA + +
+ +* Version: 1.2.2 +* GitHub: NA +* Source code: https://github.com/cran/CINNA +* Date/Publication: 2023-08-08 16:40:02 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "CINNA")` for more info + +
+ +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘circlize’ ‘utils’ + All declared Imports should be used. + ``` + +# dosearch + +
+ +* Version: 1.0.8 +* GitHub: NA +* Source code: https://github.com/cran/dosearch +* Date/Publication: 2021-08-19 16:40:02 UTC +* Number of recursive dependencies: 18 + +Run `revdepcheck::cloud_details(, "dosearch")` for more info + +
+ +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + libs 6.2Mb + ``` + +# ggnetwork + +
+ +* Version: 0.5.12 +* GitHub: https://github.com/briatte/ggnetwork +* Source code: https://github.com/cran/ggnetwork +* Date/Publication: 2023-03-06 20:00:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "ggnetwork")` for more info + +
+ +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘sna’ ‘utils’ + All declared Imports should be used. + ``` + +# inferCSN + +
+ +* Version: 0.99.8 +* GitHub: https://github.com/mengxu98/inferCSN +* Source code: https://github.com/cran/inferCSN +* Date/Publication: 2023-12-04 05:00:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "inferCSN")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 35.6Mb + sub-directories of 1Mb or more: + libs 34.6Mb + ``` + # influential
@@ -35,6 +173,186 @@ Run `revdepcheck::cloud_details(, "influential")` for more info Position: 1 Code: ... Docs: incidence ``` +# markovchain + +
+ +* Version: 0.9.5 +* GitHub: https://github.com/spedygiorgio/markovchain +* Source code: https://github.com/cran/markovchain +* Date/Publication: 2023-09-24 09:20:02 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "markovchain")` for more info + +
+ +## In both + +* checking re-building of vignette outputs ... ERROR + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘an_introduction_to_markovchain_package.Rmd’ using rmarkdown + Error: processing vignette 'an_introduction_to_markovchain_package.Rmd' failed with diagnostics: + pandoc version 2.7 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available). + --- failed re-building ‘an_introduction_to_markovchain_package.Rmd’ + + --- re-building ‘gsoc_2017_additions.Rmd’ using rmarkdown + --- finished re-building ‘gsoc_2017_additions.Rmd’ + + ... + Error: processing vignette 'higher_order_markov_chains.Rmd' failed with diagnostics: + pandoc version 2.7 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available). + --- failed re-building ‘higher_order_markov_chains.Rmd’ + + SUMMARY: processing the following files failed: + ‘an_introduction_to_markovchain_package.Rmd’ + ‘higher_order_markov_chains.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘etm’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 24.0Mb + sub-directories of 1Mb or more: + libs 21.9Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# pcalg + +
+ +* Version: 2.7-9 +* GitHub: NA +* Source code: https://github.com/cran/pcalg +* Date/Publication: 2023-09-26 05:40:03 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "pcalg")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 20.0Mb + sub-directories of 1Mb or more: + data 2.1Mb + libs 14.6Mb + ``` + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘combinat’, ‘unifDAG’ + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignette2018.Rnw’ using Sweave + Loading required package: Rgraphviz + Loading required package: graph + Loading required package: BiocGenerics + + Attaching package: 'BiocGenerics' + + The following objects are masked from 'package:stats': + + ... + l.179 \RequirePackage{grfext}\relax + ^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building 'vignette2018.Rnw' + + SUMMARY: processing the following file failed: + 'vignette2018.Rnw' + + Error: Vignette re-building failed. + Execution halted + ``` + +# phyloseqGraphTest + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/jfukuyama/phyloseqGraphTest +* Source code: https://github.com/cran/phyloseqGraphTest +* Date/Publication: 2020-02-07 16:30:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "phyloseqGraphTest")` for more info + +
+ +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘intergraph’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# shazam + +
+ +* Version: 1.2.0 +* GitHub: NA +* Source code: https://github.com/cran/shazam +* Date/Publication: 2023-10-02 18:50:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "shazam")` for more info + +
+ +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘Baseline-Vignette.Rmd’ using rmarkdown + tlmgr update --all --self + Can't locate mktexlsr.pl in @INC (@INC contains: /opt/TinyTeX/tlpkg /opt/TinyTeX/texmf-dist/scripts/texlive /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/bin/fmtutil line 26. + BEGIN failed--compilation aborted at /usr/bin/fmtutil line 28. + texlive-scripts package not found (?!), skipping revision consistency check + tlmgr: package repository https://ctan.math.illinois.edu/systems/texlive/tlnet (verified) + tlmgr install: package already present: l3backend + ! LaTeX Error: Mismatched LaTeX support files detected. + (LaTeX) Loading 'l3backend-pdftex.def' aborted! + ... + LaTeX failed to compile /tmp/workdir/shazam/new/shazam.Rcheck/vign_test/shazam/vignettes/Targeting-Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Targeting-Vignette.log for more info. + --- failed re-building ‘Targeting-Vignette.Rmd’ + + SUMMARY: processing the following files failed: + ‘Baseline-Vignette.Rmd’ ‘DistToNearest-Vignette.Rmd’ + ‘Mutation-Vignette.Rmd’ ‘Shmulate-Vignette.Rmd’ + ‘Targeting-Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + # statGraph