ggally: Extension to 'ggplot2'

adventr

Version: 0.1.8
GitHub: NA
Source code: https://github.com/cran/adventr
Date/Publication: 2020-05-05 16:50:06 UTC
Number of recursive dependencies: 165

Run revdepcheck::revdep_details(, "adventr") for more info

checking whether package ‘adventr’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘learnr’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/adventr/new/adventr.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: tutorials 5.5Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’ ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’ ‘sandwich’ ‘sjstats’ ‘tidyr’ All declared Imports should be used.

airGR

Version: 1.7.6
GitHub: NA
Source code: https://github.com/cran/airGR
Date/Publication: 2023-10-26 07:30:05 UTC
Number of recursive dependencies: 110

Run revdepcheck::revdep_details(, "airGR") for more info

checking whether package ‘airGR’ can be installed ... ERROR Installation failed. See ‘/ggally/revdep/checks.noindex/airGR/new/airGR.Rcheck/00install.out’ for details.

* installing *source* package ‘airGR’ ...
** package ‘airGR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
sh: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
using SDK: ‘MacOSX14.2.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c airGR.c -o airGR.o
/opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran  -fPIC  -Wall -g -O2  -c  frun_CEMANEIGE.f90 -o frun_CEMANEIGE.o
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
...
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
make: *** [frun_CEMANEIGE.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [frun_GR4H.o] Error 1
make: *** [frun_GR2M.o] Error 1
make: *** [frun_GR1A.o] Error 1
make: *** [frun_GR4J.o] Error 1
make: *** [frun_GR5H.o] Error 1
ERROR: compilation failed for package ‘airGR’
* removing ‘/ggally/revdep/checks.noindex/airGR/new/airGR.Rcheck/airGR’

* installing *source* package ‘airGR’ ...
** package ‘airGR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
sh: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
using SDK: ‘MacOSX14.2.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c airGR.c -o airGR.o
/opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran  -fPIC  -Wall -g -O2  -c  frun_CEMANEIGE.f90 -o frun_CEMANEIGE.o
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
...
make: *** Waiting for unfinished jobs....
make: *** [frun_GR1A.o] Error 1
make: *** [frun_GR2M.o] Error 1
make: *** [frun_GR4H.o] Error 1
make: *** [frun_GR5H.o] Error 1
make: *** [frun_GR4J.o] Error 1
make: *** [frun_GR6J.o] Error 1
make: *** [frun_GR5J.o] Error 1
ERROR: compilation failed for package ‘airGR’
* removing ‘/ggally/revdep/checks.noindex/airGR/old/airGR.Rcheck/airGR’

alevinQC

Version: 1.18.0
GitHub: https://github.com/csoneson/alevinQC
Source code: https://github.com/cran/alevinQC
Date/Publication: 2023-10-24
Number of recursive dependencies: 110

Run revdepcheck::revdep_details(, "alevinQC") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 20.5Mb sub-directories of 1Mb or more: extdata 19.2Mb

AlpsNMR

Version: 4.4.0
GitHub: https://github.com/sipss/AlpsNMR
Source code: https://github.com/cran/AlpsNMR
Date/Publication: 2023-10-24
Number of recursive dependencies: 187

Run revdepcheck::revdep_details(, "AlpsNMR") for more info

checking whether package ‘AlpsNMR’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘future’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/AlpsNMR/new/AlpsNMR.Rcheck/00install.out’ for details.

AntMAN

Version: 1.1.0
GitHub: https://github.com/bbodin/AntMAN
Source code: https://github.com/cran/AntMAN
Date/Publication: 2021-07-23 10:00:02 UTC
Number of recursive dependencies: 80

Run revdepcheck::revdep_details(, "AntMAN") for more info

checking whether package ‘AntMAN’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘mvtnorm’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/AntMAN/new/AntMAN.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rdpack’ ‘mcclust’ All declared Imports should be used.

BasketballAnalyzeR

Version: 0.5.0
GitHub: https://github.com/sndmrc/BasketballAnalyzeR
Source code: https://github.com/cran/BasketballAnalyzeR
Date/Publication: 2020-06-26 09:00:11 UTC
Number of recursive dependencies: 86

Run revdepcheck::revdep_details(, "BasketballAnalyzeR") for more info

checking whether package ‘BasketballAnalyzeR’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/BasketballAnalyzeR/new/BasketballAnalyzeR.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’ All declared Imports should be used.

BindingSiteFinder

Version: 2.0.0
GitHub: https://github.com/ZarnackGroup/BindingSiteFinder
Source code: https://github.com/cran/BindingSiteFinder
Date/Publication: 2023-10-24
Number of recursive dependencies: 218

Run revdepcheck::revdep_details(, "BindingSiteFinder") for more info

checking whether package ‘BindingSiteFinder’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘GenomicRanges’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘IRanges’ was built under R version 4.3.1 Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 See ‘/ggally/revdep/checks.noindex/BindingSiteFinder/new/BindingSiteFinder.Rcheck/00install.out’ for details.

bootcluster

Version: 0.3.2
GitHub: NA
Source code: https://github.com/cran/bootcluster
Date/Publication: 2022-01-29 22:50:03 UTC
Number of recursive dependencies: 82

Run revdepcheck::revdep_details(, "bootcluster") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘sna’ All declared Imports should be used.

CARBayes

Version: 6.1
GitHub: https://github.com/duncanplee/CARBayes
Source code: https://github.com/cran/CARBayes
Date/Publication: 2023-11-17 11:40:11 UTC
Number of recursive dependencies: 139

Run revdepcheck::revdep_details(, "CARBayes") for more info

checking whether package ‘CARBayes’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘MASS’ was built under R version 4.3.1 Warning: package ‘Rcpp’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/CARBayes/new/CARBayes.Rcheck/00install.out’ for details.

CARBayesST

Version: 4.0
GitHub: https://github.com/duncanplee/CARBayesST
Source code: https://github.com/cran/CARBayesST
Date/Publication: 2023-10-30 16:40:02 UTC
Number of recursive dependencies: 119

Run revdepcheck::revdep_details(, "CARBayesST") for more info

checking whether package ‘CARBayesST’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘MASS’ was built under R version 4.3.1 Warning: package ‘Rcpp’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/CARBayesST/new/CARBayesST.Rcheck/00install.out’ for details.

CeTF

Version: 1.14.0
GitHub: NA
Source code: https://github.com/cran/CeTF
Date/Publication: 2023-10-24
Number of recursive dependencies: 230

Run revdepcheck::revdep_details(, "CeTF") for more info

checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: data 1.5Mb doc 3.1Mb

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::revdep_details(, "CINNA") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘circlize’ ‘utils’ All declared Imports should be used.

CluMSID

Version: 1.18.0
GitHub: https://github.com/tdepke/CluMSID
Source code: https://github.com/cran/CluMSID
Date/Publication: 2023-10-24
Number of recursive dependencies: 195

Run revdepcheck::revdep_details(, "CluMSID") for more info

checking whether package ‘CluMSID’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘dbscan::as.dendrogram’ by ‘stats::as.dendrogram’ when loading ‘CluMSID’ See ‘/ggally/revdep/checks.noindex/CluMSID/new/CluMSID.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: doc 5.6Mb

clustrd

Version: 1.4.0
GitHub: NA
Source code: https://github.com/cran/clustrd
Date/Publication: 2022-07-16 23:20:06 UTC
Number of recursive dependencies: 76

Run revdepcheck::revdep_details(, "clustrd") for more info

checking whether package ‘clustrd’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/clustrd/new/clustrd.Rcheck/00install.out’ for details.

communication

Version: 0.1
GitHub: NA
Source code: https://github.com/cran/communication
Date/Publication: 2021-02-25 09:20:02 UTC
Number of recursive dependencies: 108

Run revdepcheck::revdep_details(, "communication") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’ ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’ All declared Imports should be used.

conserveR

Version: 1.0.4
GitHub: https://github.com/azizka/conserveR
Source code: https://github.com/cran/conserveR
Date/Publication: 2021-08-02 09:10:06 UTC
Number of recursive dependencies: 64

Run revdepcheck::revdep_details(, "conserveR") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘scales’ ‘sna’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 244 marked UTF-8 strings

corrViz

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/corrViz
Date/Publication: 2023-06-30 11:40:07 UTC
Number of recursive dependencies: 128

Run revdepcheck::revdep_details(, "corrViz") for more info

checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: doc 6.7Mb

coveffectsplot

Version: 1.0.5
GitHub: https://github.com/smouksassi/coveffectsplot
Source code: https://github.com/cran/coveffectsplot
Date/Publication: 2024-01-18 14:10:02 UTC
Number of recursive dependencies: 149

Run revdepcheck::revdep_details(, "coveffectsplot") for more info

checking whether package ‘coveffectsplot’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘data.table’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/coveffectsplot/new/coveffectsplot.Rcheck/00install.out’ for details.

covsim

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/covsim
Date/Publication: 2022-04-29 22:40:09 UTC
Number of recursive dependencies: 107

Run revdepcheck::revdep_details(, "covsim") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rcpp’ ‘gsl’ All declared Imports should be used.

cyanoFilter

Version: 1.10.0
GitHub: https://github.com/fomotis/cyanoFilter
Source code: https://github.com/cran/cyanoFilter
Date/Publication: 2023-10-24
Number of recursive dependencies: 146

Run revdepcheck::revdep_details(, "cyanoFilter") for more info

checking package dependencies ... ERROR ``` Package required but not available: ‘flowClust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

descriptio

Version: 1.2
GitHub: https://github.com/nicolas-robette/descriptio
Source code: https://github.com/cran/descriptio
Date/Publication: 2023-10-05 12:50:02 UTC
Number of recursive dependencies: 98

Run revdepcheck::revdep_details(, "descriptio") for more info

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘FactoMineR’, ‘vcd’

fect

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/fect
Date/Publication: 2022-10-14 09:52:32 UTC
Number of recursive dependencies: 81

Run revdepcheck::revdep_details(, "fect") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘panelView’ All declared Imports should be used.

fic

Version: 1.0.0
GitHub: https://github.com/chjackson/fic
Source code: https://github.com/cran/fic
Date/Publication: 2019-04-13 08:32:39 UTC
Number of recursive dependencies: 119

Run revdepcheck::revdep_details(, "fic") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘numDeriv’ All declared Imports should be used.

finalfit

Version: 1.0.7
GitHub: https://github.com/ewenharrison/finalfit
Source code: https://github.com/cran/finalfit
Date/Publication: 2023-11-16 17:40:02 UTC
Number of recursive dependencies: 172

Run revdepcheck::revdep_details(, "finalfit") for more info

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: doc 4.9Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tidyselect’ All declared Imports should be used.

fingerPro

Version: 1.1
GitHub: https://github.com/NA/NA
Source code: https://github.com/cran/fingerPro
Date/Publication: 2018-08-28 10:04:54 UTC
Number of recursive dependencies: 161

Run revdepcheck::revdep_details(, "fingerPro") for more info

checking whether package ‘fingerPro’ can be installed ... ERROR Installation failed. See ‘/ggally/revdep/checks.noindex/fingerPro/new/fingerPro.Rcheck/00install.out’ for details.

* installing *source* package ‘fingerPro’ ...
** package ‘fingerPro’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX14.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/ggally/revdep/library.noindex/fingerPro/Rcpp/include' -I'/ggally/revdep/library.noindex/fingerPro/RcppGSL/include' -I'/ggally/revdep/library.noindex/fingerPro/RcppProgress/include' -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/ggally/revdep/library.noindex/fingerPro/Rcpp/include' -I'/ggally/revdep/library.noindex/fingerPro/RcppGSL/include' -I'/ggally/revdep/library.noindex/fingerPro/RcppProgress/include' -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c fingerprinting.cpp -o fingerprinting.o
In file included from RcppExports.cpp:4:
In file included from /ggally/revdep/library.noindex/fingerPro/RcppGSL/include/RcppGSL.h:25:
...
make: *** Waiting for unfinished jobs....
In file included from fingerprinting.cpp:5:
In file included from /ggally//ggally/revdep/library.noindex/fingerPro/RcppGSL/include/RcppGSL.h:25:
/ggally/revdep/library.noindex/fingerPro/RcppGSL/include/RcppGSLForward.h:25:10: fatal error: 'gsl/gsl_vector.h' file not found
#include <gsl/gsl_vector.h>
         ^~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [fingerprinting.o] Error 1
ERROR: compilation failed for package ‘fingerPro’
* removing ‘/ggally/revdep/checks.noindex/fingerPro/new/fingerPro.Rcheck/fingerPro’

* installing *source* package ‘fingerPro’ ...
** package ‘fingerPro’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX14.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/ggally//ggally/revdep/library.noindex/fingerPro/Rcpp/include' -I'/ggally/revdep/library.noindex/fingerPro/RcppGSL/include' -I'/ggally//ggally/revdep/library.noindex/fingerPro/RcppProgress/include' -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/ggally/revdep/library.noindex/fingerPro/Rcpp/include' -I'/ggally/revdep/library.noindex/fingerPro/RcppGSL/include' -I'/ggally/revdep/library.noindex/fingerPro/RcppProgress/include' -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c fingerprinting.cpp -o fingerprinting.o
In file included from RcppExports.cpp:4:
In file included from /ggally/revdep/library.noindex/fingerPro/RcppGSL/include/RcppGSL.h:25:
...
make: *** Waiting for unfinished jobs....
In file included from fingerprinting.cpp:5:
In file included from /ggally/revdep/library.noindex/fingerPro/RcppGSL/include/RcppGSL.h:25:
/ggally/revdep/library.noindex/fingerPro/RcppGSL/include/RcppGSLForward.h:25:10: fatal error: 'gsl/gsl_vector.h' file not found
#include <gsl/gsl_vector.h>
         ^~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [fingerprinting.o] Error 1
ERROR: compilation failed for package ‘fingerPro’
* removing ‘/ggally/revdep/checks.noindex/fingerPro/old/fingerPro.Rcheck/fingerPro’

FPDclustering

Version: 2.3.1
GitHub: NA
Source code: https://github.com/cran/FPDclustering
Date/Publication: 2024-01-30 00:10:06 UTC
Number of recursive dependencies: 104

Run revdepcheck::revdep_details(, "FPDclustering") for more info

checking whether package ‘FPDclustering’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘mvtnorm’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/FPDclustering/new/FPDclustering.Rcheck/00install.out’ for details.

fpp2

Version: 2.5
GitHub: https://github.com/robjhyndman/fpp2-package
Source code: https://github.com/cran/fpp2
Date/Publication: 2023-02-19 07:30:02 UTC
Number of recursive dependencies: 83

Run revdepcheck::revdep_details(, "fpp2") for more info

checking whether package ‘fpp2’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/fpp2/new/fpp2.Rcheck/00install.out’ for details.

freqparcoord

Version: 1.0.1
GitHub: NA
Source code: https://github.com/cran/freqparcoord
Date/Publication: 2016-01-17 10:59:33
Number of recursive dependencies: 60

Run revdepcheck::revdep_details(, "freqparcoord") for more info

checking whether package ‘freqparcoord’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 Warning: package ‘FNN’ was built under R version 4.3.1 Warning: package ‘mvtnorm’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/freqparcoord/new/freqparcoord.Rcheck/00install.out’ for details.

gatom

Version: 1.0.0
GitHub: https://github.com/ctlab/gatom
Source code: https://github.com/cran/gatom
Date/Publication: 2023-10-24
Number of recursive dependencies: 150

Run revdepcheck::revdep_details(, "gatom") for more info

checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘htmlwidgets:::createWidgetId’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .makeEdgeTable: no visible binding for global variable ‘gene’ .makeEdgeTable: no visible binding for global variable ‘ID’ .makeEdgeTable: no visible binding for global variable ‘pval’ .makeEdgeTable: no visible binding for global variable ‘enzyme’ .makeEdgeTable: no visible binding for global variable ‘reaction’ .makeEdgeTable: no visible binding for global variable ‘origin’ .makeEdgeTable: no visible binding for global variable ‘atom.x’ .makeEdgeTable: no visible binding for global variable ‘atom.y’ .makeVertexTable: no visible binding for global variable ‘ID’ .makeVertexTable: no visible binding for global variable ‘pval’ ... Undefined global functions or variables: ID PATHNAME aggregate atom atom.x atom.y base_metabolite dev.off enzyme from gene keys metabolite metabolite.x metabolite.y na.omit name organism origin pdf pval reaction read.table rgb setNames signal signalRank species symbol tail to Consider adding importFrom("grDevices", "dev.off", "pdf", "rgb") importFrom("stats", "aggregate", "na.omit", "setNames") importFrom("utils", "read.table", "tail") to your NAMESPACE file.

GENESIS

Version: 2.32.0
GitHub: https://github.com/UW-GAC/GENESIS
Source code: https://github.com/cran/GENESIS
Date/Publication: 2023-10-24
Number of recursive dependencies: 195

Run revdepcheck::revdep_details(, "GENESIS") for more info

checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: doc 3.2Mb extdata 3.1Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘survey:::saddle’ See the note in ?`:::` about the use of this operator.

GeomxTools

Version: 3.6.2
GitHub: NA
Source code: https://github.com/cran/GeomxTools
Date/Publication: 2024-02-09
Number of recursive dependencies: 229

Run revdepcheck::revdep_details(, "GeomxTools") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_GeoMxSet_probeCollapse.R:61:3'): test that collapsed probe count is equal to the geomean of probes for each target ── sum(matches) == nrow(aggTestData@assayData$exprs) * numDCC is not TRUE

actual: FALSE expected: TRUE ── Failure ('test_GeoMxSet_probeCollapse.R:100:3'): test that the geomean and geosd of negatives is correct ── sum(matches) == length(unique(PKC$Module)) * numDCC * 2 is not TRUE

actual: FALSE expected: TRUE

[ FAIL 2 | WARN 16 | SKIP 0 | PASS 288 ] Error: Test failures Execution halted ```
checking whether package ‘GeomxTools’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘Biobase’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘NanoStringNCTools’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/GeomxTools/new/GeomxTools.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 24.5Mb sub-directories of 1Mb or more: doc 5.2Mb extdata 18.4Mb
checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE aggregateCounts: no visible binding for global variable ‘TargetName’ hkNorm: no visible binding for global variable ‘TargetName’ mixedModelDE: multiple local function definitions for ‘deFunc’ with different formal arguments qgrubbs: no visible global function definition for ‘qtable’ readPKCFile: no visible binding for global variable ‘RTS_ID’ readPKCFile: no visible binding for global variable ‘Module’ setGrubbsFlags: no visible binding for global variable ‘TargetName’ setGrubbsFlags : <anonymous>: no visible binding for global variable ‘Module’ ... variable ‘Module’ setSignatureFuncs<-,NanoStringGeoMxSet-character: no visible global function definition for ‘setSigFuncs<-’ signatureScores,NanoStringGeoMxSet: no visible global function definition for ‘assayDataElement2’ signatureScores,NanoStringGeoMxSet: no visible global function definition for ‘.sigCalc’ Undefined global functions or variables: .sigCalc Module RTS_ID TargetName analtye assayDataElement2 qtable setSigFuncs<-

gfilmm

Version: 2.0.5
GitHub: https://github.com/stla/gfilmm
Source code: https://github.com/cran/gfilmm
Date/Publication: 2022-07-11 23:20:06 UTC
Number of recursive dependencies: 134

Run revdepcheck::revdep_details(, "gfilmm") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

ggbio

Version: 1.50.0
GitHub: https://github.com/lawremi/ggbio
Source code: https://github.com/cran/ggbio
Date/Publication: 2023-11-01
Number of recursive dependencies: 186

Run revdepcheck::revdep_details(, "ggbio") for more info

checking examples ... ERROR ``` Running examples in ‘ggbio-Ex.R’ failed The error most likely occurred in:

Name: autoplot

Title: Generic autoplot function

Aliases: autoplot autoplot,GRanges-method autoplot,GRangesList-method

autoplot,IRanges-method autoplot,Seqinfo-method

autoplot,BSgenome-method autoplot,GAlignments-method

autoplot,BamFile-method autoplot,BamFileList-method

autoplot,TxDbOREnsDb-method autoplot,character-method

...

End(Not run)

code chunk number 56: bs-v

library(BSgenome.Hsapiens.UCSC.hg19) Error in library(BSgenome.Hsapiens.UCSC.hg19) : there is no package called 'BSgenome.Hsapiens.UCSC.hg19' Execution halted ```
checking whether package ‘ggbio’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/ggbio/new/ggbio.Rcheck/00install.out’ for details.
checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '+' and siglist 'Tracks,ANY' generic '+' and siglist 'Tracks,Tracks' generic '+' and siglist 'Tracks,cartesian' generic '+' and siglist 'Tracks,position_c' generic '+' and siglist 'Tracks,theme' generic '+' and siglist 'Tracks,zoom' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'geom_alignment': \S4method{geom_alignment}{GRanges} Code: function(data, ..., xlab, ylab, main, facets = NULL, stat = c("stepping", "identity"), range.geom = c("rect", "arrowrect"), gap.geom = c("chevron", "arrow", "segment"), rect.height = NULL, group.selfish = TRUE) Docs: function(data, ..., xlab, ylab, main, facets = NULL, stat = c("stepping", "identity"), range.geom = c("rect", "arrowrect"), gap.geom = c("chevron", "arrow", "segment"), rect.height = NULL, group.selfish = TRUE, ... NULL, scale = 1, width = NA, height = NA, units = c("in", "cm", "mm"), dpi = 300, limitsize = TRUE, ...) Docs: function(filename, plot = last_plot(), device = default_device(filename), path = NULL, scale = 1, width = par("din")[1], height = par("din")[2], units = c("in", "cm", "mm"), dpi = 300, limitsize = TRUE, ...) Mismatches in argument default values: Name: 'device' Code: NULL Docs: default_device(filename) Name: 'width' Code: NA Docs: par("din")[1] Name: 'height' Code: NA Docs: par("din")[2]
checking package dependencies ... NOTE Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
checking dependencies in R code ... NOTE ':::' call which should be '::': 'ggplot2:::set_last_plot' See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: 'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion' 'ggplot2:::rescale01' See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .combineNames: no visible binding for global variable '.layout_circle.stats' Ideogram: no visible global function definition for 'data' Ideogram: no visible binding for global variable 'ideoCyto' getNR: no visible global function definition for 'se' getNR: no visible global function definition for 'indexProbesProcessed' getNR: no visible global function definition for 'coefs' scale_x_sequnit: no visible binding for global variable '.x' autoplot,ExpressionSet: no visible binding for global variable 'variable' ... stat_mismatch,GRanges: no visible binding for global variable 'sts' stat_mismatch,GRanges: no visible binding for global variable 'eds' stat_mismatch,GRanges: no visible binding for global variable 'read' Undefined global functions or variables: .fragLength .layout_circle.stats .x coefs data eds fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se stepping sts value variable x xend y2 yend2 Consider adding importFrom("utils", "data") to your NAMESPACE file.
checking Rd files ... NOTE checkRd: (-1) autoplot-method.Rd:445: Escaped LaTeX specials: \~

ggmcmc

Version: 1.5.1.1
GitHub: https://github.com/xfim/ggmcmc
Source code: https://github.com/cran/ggmcmc
Date/Publication: 2021-02-10 10:50:10 UTC
Number of recursive dependencies: 86

Run revdepcheck::revdep_details(, "ggmcmc") for more info

checking whether package ‘ggmcmc’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘dplyr’ was built under R version 4.3.1 Warning: package ‘tidyr’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/ggmcmc/new/ggmcmc.Rcheck/00install.out’ for details.

GGMncv

Version: 2.1.1
GitHub: https://github.com/donaldRwilliams/GGMncv
Source code: https://github.com/cran/GGMncv
Date/Publication: 2021-12-15 07:40:28 UTC
Number of recursive dependencies: 184

Run revdepcheck::revdep_details(, "GGMncv") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rdpack’ ‘mathjaxr’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \& checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&

GGMnonreg

Version: 1.0.0
GitHub: NA
Source code: https://github.com/cran/GGMnonreg
Date/Publication: 2021-04-08 11:30:06 UTC
Number of recursive dependencies: 133

Run revdepcheck::revdep_details(, "GGMnonreg") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Matrix’ ‘Rdpack’ All declared Imports should be used.
checking Rd files ... NOTE checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&

GGPA

Version: 1.14.0
GitHub: https://github.com/dongjunchung/GGPA
Source code: https://github.com/cran/GGPA
Date/Publication: 2023-10-24
Number of recursive dependencies: 88

Run revdepcheck::revdep_details(, "GGPA") for more info

checking whether package ‘GGPA’ can be installed ... WARNING Found the following significant warnings: 3_Param.cpp:74:12: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical] Warning: package ‘ggplot2’ was built under R version 4.3.1 Warning: package ‘network’ was built under R version 4.3.1 Warning: package ‘sna’ was built under R version 4.3.1 Warning: package ‘scales’ was built under R version 4.3.1 Warning: package ‘matrixStats’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/GGPA/new/GGPA.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘network’ ‘scales’ ‘sna’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking compiled code ... NOTE ``` File ‘GGPA/libs/GGPA.so’: Found ‘ZNSt314coutE’, possibly from ‘std::cout’ (C++) Object: ‘3_Param.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

ggpcp

Version: 0.2.0
GitHub: https://github.com/heike/ggpcp
Source code: https://github.com/cran/ggpcp
Date/Publication: 2022-11-28 09:30:08 UTC
Number of recursive dependencies: 93

Run revdepcheck::revdep_details(, "ggpcp") for more info

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ggdensity’

ggpicrust2

Version: 1.7.3
GitHub: https://github.com/cafferychen777/ggpicrust2
Source code: https://github.com/cran/ggpicrust2
Date/Publication: 2023-11-08 16:10:02 UTC
Number of recursive dependencies: 249

Run revdepcheck::revdep_details(, "ggpicrust2") for more info

checking package dependencies ... ERROR ``` Package required but not available: ‘MicrobiomeStat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

ggPMX

Version: 1.2.11
GitHub: https://github.com/ggPMXdevelopment/ggPMX
Source code: https://github.com/cran/ggPMX
Date/Publication: 2023-11-30 16:10:06 UTC
Number of recursive dependencies: 181

Run revdepcheck::revdep_details(, "ggPMX") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘lixoftConnectors’
checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: doc 1.1Mb help 2.4Mb testdata 4.8Mb

ggquickeda

Version: 0.3.1
GitHub: https://github.com/smouksassi/ggquickeda
Source code: https://github.com/cran/ggquickeda
Date/Publication: 2024-01-15 10:20:02 UTC
Number of recursive dependencies: 188

Run revdepcheck::revdep_details(, "ggquickeda") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘ggpmisc’ ‘ggpubr’ ‘glue’ ‘gridExtra’ ‘markdown’ ‘patchwork’ ‘plotly’ ‘quantreg’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘table1’ ‘zoo’ All declared Imports should be used.

glancedata

Version: 1.0.1
GitHub: NA
Source code: https://github.com/cran/glancedata
Date/Publication: 2019-11-22 23:10:05 UTC
Number of recursive dependencies: 109

Run revdepcheck::revdep_details(, "glancedata") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

gsynth

Version: 1.2.1
GitHub: NA
Source code: https://github.com/cran/gsynth
Date/Publication: 2021-08-06 07:50:05 UTC
Number of recursive dependencies: 77

Run revdepcheck::revdep_details(, "gsynth") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

ibawds

Version: 0.5.0
GitHub: https://github.com/stibu81/ibawds
Source code: https://github.com/cran/ibawds
Date/Publication: 2022-06-17 08:20:07 UTC
Number of recursive dependencies: 199

Run revdepcheck::revdep_details(, "ibawds") for more info

checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

ICSClust

Version: 0.1.0
GitHub: https://github.com/AuroreAA/ICSClust
Source code: https://github.com/cran/ICSClust
Date/Publication: 2023-09-21 13:20:02 UTC
Number of recursive dependencies: 137

Run revdepcheck::revdep_details(, "ICSClust") for more info

checking whether package ‘ICSClust’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ICS’ was built under R version 4.3.1 Warning: package ‘mvtnorm’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/ICSClust/new/ICSClust.Rcheck/00install.out’ for details.

ICtest

Version: 0.3-5
GitHub: NA
Source code: https://github.com/cran/ICtest
Date/Publication: 2022-05-18 07:30:29 UTC
Number of recursive dependencies: 97

Run revdepcheck::revdep_details(, "ICtest") for more info

checking whether package ‘ICtest’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘JADE’ was built under R version 4.3.1 Warning: package ‘ICS’ was built under R version 4.3.1 Warning: package ‘mvtnorm’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/ICtest/new/ICtest.Rcheck/00install.out’ for details.

InflectSSP

Version: 1.6
GitHub: NA
Source code: https://github.com/cran/InflectSSP
Date/Publication: 2023-04-19 08:00:03 UTC
Number of recursive dependencies: 97

Run revdepcheck::revdep_details(, "InflectSSP") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘svglite’ All declared Imports should be used.

isomiRs

Version: 1.30.0
GitHub: https://github.com/lpantano/isomiRs
Source code: https://github.com/cran/isomiRs
Date/Publication: 2023-10-24
Number of recursive dependencies: 173

Run revdepcheck::revdep_details(, "isomiRs") for more info

checking whether package ‘isomiRs’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 Warning: package ‘MatrixGenerics’ was built under R version 4.3.1 Warning: package ‘matrixStats’ was built under R version 4.3.1 Warning: package ‘GenomicRanges’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘IRanges’ was built under R version 4.3.1 Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 Warning: package ‘Biobase’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/isomiRs/new/isomiRs.Rcheck/00install.out’ for details.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE .clean_noise: no visible binding for global variable ‘total’ .clean_noise: no visible binding for global variable ‘hits’ .remove_gt_n_changes: no visible binding for global variable ‘changes’ isoAnnotate: no visible binding for global variable ‘pct’ isoCounts: no visible global function definition for ‘as.tibble’ isoPlot: no visible binding for global variable ‘iso_sample’ isoPlotPosition: no visible binding for global variable ‘iso_sample’ mirna2targetscan: no visible binding for global variable ‘targetscan.Hs.egMIRNA’ mirna2targetscan: no visible binding for global variable ... mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egTARGETS’ mirna2targetscan: no visible binding for global variable ‘targetscan.Mm.egTARGETSFULL’ Undefined global functions or variables: as.tibble changes hits iso_sample pct targetscan.Hs.egMIRBASE2FAMILY targetscan.Hs.egMIRNA targetscan.Hs.egTARGETS targetscan.Hs.egTARGETSFULL targetscan.Mm.egMIRBASE2FAMILY targetscan.Mm.egMIRNA targetscan.Mm.egTARGETS targetscan.Mm.egTARGETSFULL total

ITNr

Version: 0.7.0
GitHub: NA
Source code: https://github.com/cran/ITNr
Date/Publication: 2023-03-31 14:10:11 UTC
Number of recursive dependencies: 95

Run revdepcheck::revdep_details(, "ITNr") for more info

checking whether package ‘ITNr’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘network’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/ITNr/new/ITNr.Rcheck/00install.out’ for details.

jmv

Version: 2.4.11
GitHub: https://github.com/jamovi/jmv
Source code: https://github.com/cran/jmv
Date/Publication: 2023-10-12 13:20:02 UTC
Number of recursive dependencies: 192

Run revdepcheck::revdep_details(, "jmv") for more info

checking installed package size ... NOTE installed size is 10.8Mb sub-directories of 1Mb or more: R 4.0Mb i18n 6.5Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’ ‘afex’ ‘car’ ‘dplyr’ ‘emmeans’ ‘ggrepel’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’ ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’ All declared Imports should be used.

klovan

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/klovan
Date/Publication: 2024-02-01 10:20:02 UTC
Number of recursive dependencies: 136

Run revdepcheck::revdep_details(, "klovan") for more info

checking package dependencies ... NOTE Package suggested but not available for checking: ‘RGeostats’

loon.ggplot

Version: 1.3.3
GitHub: https://github.com/great-northern-diver/loon.ggplot
Source code: https://github.com/cran/loon.ggplot
Date/Publication: 2022-11-12 22:30:02 UTC
Number of recursive dependencies: 117

Run revdepcheck::revdep_details(, "loon.ggplot") for more info

checking whether package ‘loon.ggplot’ can be installed ... ERROR Installation failed. See ‘/ggally/revdep/checks.noindex/loon.ggplot/new/loon.ggplot.Rcheck/00install.out’ for details.

* installing *source* package ‘loon.ggplot’ ...
** package ‘loon.ggplot’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘loon’:
 .onLoad failed in loadNamespace() for 'loon', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] couldn't connect to display "".
In addition: Warning message:
In fun(libname, pkgname) : couldn't connect to display ""
Execution halted
ERROR: lazy loading failed for package ‘loon.ggplot’
* removing ‘/ggally/revdep/checks.noindex/loon.ggplot/new/loon.ggplot.Rcheck/loon.ggplot’

* installing *source* package ‘loon.ggplot’ ...
** package ‘loon.ggplot’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘loon’:
 .onLoad failed in loadNamespace() for 'loon', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] couldn't connect to display "".
In addition: Warning message:
In fun(libname, pkgname) : couldn't connect to display ""
Execution halted
ERROR: lazy loading failed for package ‘loon.ggplot’
* removing ‘/ggally/revdep/checks.noindex/loon.ggplot/old/loon.ggplot.Rcheck/loon.ggplot’

MAINT.Data

Version: 2.7.1
GitHub: NA
Source code: https://github.com/cran/MAINT.Data
Date/Publication: 2023-04-04 08:10:02 UTC
Number of recursive dependencies: 90

Run revdepcheck::revdep_details(, "MAINT.Data") for more info

checking whether package ‘MAINT.Data’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘Rcpp’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/MAINT.Data/new/MAINT.Data.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: R 2.1Mb data 2.3Mb

MAST

Version: 1.28.0
GitHub: https://github.com/RGLab/MAST
Source code: https://github.com/cran/MAST
Date/Publication: 2023-10-24
Number of recursive dependencies: 226

Run revdepcheck::revdep_details(, "MAST") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ══ Skipped tests (5) ═══════════════════════════════════════════════════════════ • empty test (5): 'test-GSEA-by-boot.R:99:1', 'test-SingleCellAssay.R:298:1', 'test-lmWrapper-glmer.R:8:1', 'test-sparsematrix.R:18:1', 'test-sparsematrix.R:26:1'

══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-lrtest.R:25:5'): LRT and zlm are equivalent ────────────────── all(lrout$lrstat[smallDOF] >= lrout2[smallDOF, 3, 1]) is not TRUE

actual: FALSE expected: TRUE

[ FAIL 1 | WARN 8 | SKIP 5 | PASS 292 ] Error: Test failures Execution halted ```
checking whether package ‘MAST’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘SingleCellExperiment’ was built under R version 4.3.2 Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 Warning: package ‘MatrixGenerics’ was built under R version 4.3.1 Warning: package ‘matrixStats’ was built under R version 4.3.1 Warning: package ‘GenomicRanges’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘IRanges’ was built under R version 4.3.1 Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 Warning: package ‘Biobase’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/MAST/new/MAST.Rcheck/00install.out’ for details.
checking dependencies in R code ... WARNING Missing or unexported object: ‘gdata::xls2csv’
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 10.3Mb sub-directories of 1Mb or more: data 3.7Mb doc 5.3Mb

MCbiclust

Version: 1.26.0
GitHub: NA
Source code: https://github.com/cran/MCbiclust
Date/Publication: 2023-10-24
Number of recursive dependencies: 214

Run revdepcheck::revdep_details(, "MCbiclust") for more info

checking installed package size ... NOTE installed size is 9.6Mb sub-directories of 1Mb or more: data 3.1Mb doc 5.6Mb

mgcViz

Version: 0.1.11
GitHub: https://github.com/mfasiolo/mgcViz
Source code: https://github.com/cran/mgcViz
Date/Publication: 2023-10-06 10:50:02 UTC
Number of recursive dependencies: 122

Run revdepcheck::revdep_details(, "mgcViz") for more info

checking whether package ‘mgcViz’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘mgcv’ was built under R version 4.3.1 Warning: package ‘nlme’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/mgcViz/new/mgcViz.Rcheck/00install.out’ for details.

miaSim

Version: 1.8.0
GitHub: https://github.com/microbiome/miaSim
Source code: https://github.com/cran/miaSim
Date/Publication: 2023-10-24
Number of recursive dependencies: 206

Run revdepcheck::revdep_details(, "miaSim") for more info

checking whether package ‘miaSim’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘TreeSummarizedExperiment’ was built under R version 4.3.1 Warning: package ‘SingleCellExperiment’ was built under R version 4.3.2 Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 Warning: package ‘MatrixGenerics’ was built under R version 4.3.1 Warning: package ‘matrixStats’ was built under R version 4.3.1 Warning: package ‘GenomicRanges’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘IRanges’ was built under R version 4.3.1 Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 Warning: package ‘Biobase’ was built under R version 4.3.1 Warning: package ‘Biostrings’ was built under R version 4.3.2 Warning: package ‘XVector’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/miaSim/new/miaSim.Rcheck/00install.out’ for details.

mlergm

Version: 0.8
GitHub: NA
Source code: https://github.com/cran/mlergm
Date/Publication: 2021-08-23 16:00:02 UTC
Number of recursive dependencies: 94

Run revdepcheck::revdep_details(, "mlergm") for more info

checking whether package ‘mlergm’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ergm’ was built under R version 4.3.1 Warning: package ‘network’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/mlergm/new/mlergm.Rcheck/00install.out’ for details.

mlrMBO

Version: 1.1.5.1
GitHub: https://github.com/mlr-org/mlrMBO
Source code: https://github.com/cran/mlrMBO
Date/Publication: 2022-07-04 08:50:50 UTC
Number of recursive dependencies: 142

Run revdepcheck::revdep_details(, "mlrMBO") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: (https://mlr3.mlr-org.com). Due to the focus on 'mlr3' there might be uncaught bugs meanwhile in {mlr} - please consider switching. Loading required package: smoof Loading required package: checkmate [ FAIL 1 | WARN 0 | SKIP 0 | PASS 59 ]

══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_mbo_km.R:47:3'): mbo works with km ─────────────────────────── suppressPackageStartupMessages(...) produced warnings.

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 59 ] Error: Test failures In addition: Warning message: package 'checkmate' was built under R version 4.3.1 Execution halted ```
checking whether package ‘mlrMBO’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘checkmate’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/mlrMBO/new/mlrMBO.Rcheck/00install.out’ for details.

MOFA2

Version: 1.12.1
GitHub: https://github.com/bioFAM/MOFA2
Source code: https://github.com/cran/MOFA2
Date/Publication: 2024-01-05
Number of recursive dependencies: 259

Run revdepcheck::revdep_details(, "MOFA2") for more info

checking examples ... ERROR ``` Running examples in ‘MOFA2-Ex.R’ failed The error most likely occurred in:

Name: plot_dimred

Title: Plot dimensionality reduction based on MOFA factors

Aliases: plot_dimred

** Examples

Using an existing trained model on simulated data

file <- system.file("extdata", "model.hdf5", package = "MOFA2") model <- load_model(file)

Run UMAP

model <- run_umap(model) Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : function 'as_cholmod_sparse' not provided by package 'Matrix' Calls: run_umap ... irlba_tsvd_normalized_laplacian_init -> irlba_spectral_tsvd Execution halted ```
checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'create_mofa_from_Seurat': create_mofa_from_Seurat Code: function(seurat, groups = NULL, assays = NULL, layer = "data", features = NULL, extract_metadata = FALSE) Docs: function(seurat, groups = NULL, assays = NULL, slot = "scale.data", features = NULL, extract_metadata = FALSE) Argument names in code not in docs: layer Argument names in docs not in code: slot Mismatches in argument names: Position: 4 Code: layer Docs: slot
checking whether package ‘MOFA2’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/ggally/revdep/checks.noindex/MOFA2/new/MOFA2.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: doc 4.7Mb extdata 2.0Mb
checking R code for possible problems ... NOTE .plot_factors_vs_cov_1d: no visible binding for global variable ‘value.factor’ .plot_factors_vs_cov_1d: no visible binding for global variable ‘value_scaled’ .plot_factors_vs_cov_1d: no visible binding for global variable ‘value.covariate’ .plot_factors_vs_cov_1d: no visible binding for global variable ‘value’ .plot_factors_vs_cov_2d: no visible binding for global variable ‘value.factor’ .set_xax: no visible binding for global variable ‘value’ ... plot_weights: no visible binding for global variable ‘value’ plot_weights: no visible binding for global variable ‘.’ summarise_factors: no visible binding for global variable ‘value’ summarise_factors: no visible binding for global variable ‘level’ summarise_factors: no visible binding for global variable ‘group’ Undefined global functions or variables: . CreateDimReducObject E2 L1 L2 colData covariate covariate_value feature.statistic group group_label level ntotal pathway ptotal sample_id sharedness smoothness value value.covariate value.factor value.unaligned value.warped value_scaled variance view ymax ymin
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘PCGSE’

NetworkChange

Version: 0.8
GitHub: https://github.com/jongheepark/NetworkChange
Source code: https://github.com/cran/NetworkChange
Date/Publication: 2022-03-04 07:30:02 UTC
Number of recursive dependencies: 132

Run revdepcheck::revdep_details(, "NetworkChange") for more info

checking whether package ‘NetworkChange’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘MCMCpack’ was built under R version 4.3.1 Warning: package ‘coda’ was built under R version 4.3.1 Warning: package ‘MASS’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/NetworkChange/new/NetworkChange.Rcheck/00install.out’ for details.
checking Rd files ... NOTE checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \& checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \& checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&

NPflow

Version: 0.13.5
GitHub: https://github.com/sistm/NPflow
Source code: https://github.com/cran/NPflow
Date/Publication: 2024-01-13 10:00:02 UTC
Number of recursive dependencies: 70

Run revdepcheck::revdep_details(, "NPflow") for more info

checking whether package ‘NPflow’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘Rcpp’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/NPflow/new/NPflow.Rcheck/00install.out’ for details.

nzelect

Version: 0.4.0
GitHub: NA
Source code: https://github.com/cran/nzelect
Date/Publication: 2017-10-02 20:35:23 UTC
Number of recursive dependencies: 95

Run revdepcheck::revdep_details(, "nzelect") for more info

checking data for non-ASCII characters ... NOTE Note: found 6409 marked UTF-8 strings

pareg

Version: 1.6.0
GitHub: https://github.com/cbg-ethz/pareg
Source code: https://github.com/cran/pareg
Date/Publication: 2023-10-24
Number of recursive dependencies: 320

Run revdepcheck::revdep_details(, "pareg") for more info

R CMD check timed out
checking whether package ‘pareg’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘tensorflow’ was built under R version 4.3.1 Found the following additional notes/warnings: Non-staged installation was used See ‘/ggally/revdep/checks.noindex/pareg/new/pareg.Rcheck/00install.out’ for details.
checking for portable file names ... NOTE ``` Found the following non-portable file paths: pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/config.yaml ... pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/config.yaml pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/params.csv pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/workflow/scripts/compare_rocauc_vs_loss.R pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter

Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ```

PAsso

Version: 0.1.10
GitHub: https://github.com/XiaoruiZhu/PAsso
Source code: https://github.com/cran/PAsso
Date/Publication: 2021-06-18 09:20:08 UTC
Number of recursive dependencies: 180

Run revdepcheck::revdep_details(, "PAsso") for more info

checking whether package ‘PAsso’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 Warning: package ‘dplyr’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/PAsso/new/PAsso.Rcheck/00install.out’ for details.

PhosR

Version: 1.12.0
GitHub: NA
Source code: https://github.com/cran/PhosR
Date/Publication: 2023-10-24
Number of recursive dependencies: 193

Run revdepcheck::revdep_details(, "PhosR") for more info

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: data 3.3Mb doc 2.2Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘stringi’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE abundPlot: no visible binding for global variable ‘.’ Undefined global functions or variables: .

Pi

Version: 2.14.0
GitHub: https://github.com/hfang-bristol/Pi
Source code: https://github.com/cran/Pi
Date/Publication: 2023-10-24
Number of recursive dependencies: 260

Run revdepcheck::revdep_details(, "Pi") for more info

checking package dependencies ... ERROR ``` Package required but not available: ‘dnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

plotly

Version: 4.10.4
GitHub: https://github.com/plotly/plotly.R
Source code: https://github.com/cran/plotly
Date/Publication: 2024-01-13 22:40:02 UTC
Number of recursive dependencies: 148

Run revdepcheck::revdep_details(, "plotly") for more info

checking whether package ‘plotly’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/plotly/new/plotly.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: R 1.0Mb htmlwidgets 4.0Mb

PopGenReport

Version: 3.1
GitHub: https://github.com/green-striped-gecko/PopGenReport
Source code: https://github.com/cran/PopGenReport
Date/Publication: 2023-10-11 07:20:02 UTC
Number of recursive dependencies: 141

Run revdepcheck::revdep_details(, "PopGenReport") for more info

checking whether package ‘PopGenReport’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘knitr’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/PopGenReport/new/PopGenReport.Rcheck/00install.out’ for details.

protGear

Version: 1.6.0
GitHub: https://github.com/Keniajin/protGear
Source code: https://github.com/cran/protGear
Date/Publication: 2023-10-24
Number of recursive dependencies: 203

Run revdepcheck::revdep_details(, "protGear") for more info

checking whether package ‘protGear’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘dplyr’ was built under R version 4.3.1 Warning: package ‘limma’ was built under R version 4.3.1 Warning: package ‘vsn’ was built under R version 4.3.1 Warning: package ‘Biobase’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/protGear/new/protGear.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: doc 3.9Mb extdata 1.2Mb
checking R code for possible problems ... NOTE best_CV_estimation: no visible binding for global variable ‘x’ best_CV_estimation: no visible binding for global variable ‘prop’ best_CV_estimation: no visible binding for global variable ‘val’ best_CV_estimation: no visible binding for global variable ‘meanX1_X2’ best_CV_estimation: no visible binding for global variable ‘meanX2_X3’ best_CV_estimation: no visible binding for global variable ‘xbar’ best_CV_estimation: no visible binding for global variable ‘CVX’ best_CV_estimation: no visible binding for global variable ‘meanX’ best_CV_estimation: no visible binding for global variable ‘selected’ best_CV_estimation: no visible binding for global variable ‘CVX2_X3’ ... visualize_slide_2d: no visible binding for global variable ‘meanY’ Undefined global functions or variables: .id Array BGMedian BG_Median Block CVX CVX1_X2 CVX1_X3 CVX2_X3 Column Description FBG_Median FMedian FMedianBG_correct MFI MFI_val Name Row TAG TAG_mfi TAG_name X Y antigen antigen_name best_CV buffers day_batches global_BGMedian index log_bg log_fb machines meanBest2_RLM meanX meanX1_X2 meanX1_X3 meanX2_X3 meanY mean_all_anti mean_mfi minimum_BGMedian prop rank_mean_all_anti sampleID sampleID2 sample_array_ID sample_index sdX sdX1_X2 sdX1_X3 sdX2_X3 sd_mfi selected slide stdev_all_anti temp v1 v2 val value variable x xbar

randomForestExplainer

Version: 0.10.1
GitHub: https://github.com/ModelOriented/randomForestExplainer
Source code: https://github.com/cran/randomForestExplainer
Date/Publication: 2020-07-11 20:30:02 UTC
Number of recursive dependencies: 105

Run revdepcheck::revdep_details(, "randomForestExplainer") for more info

checking LazyData ... NOTE 'LazyData' is specified without a 'data' directory

rbioacc

Version: 1.2-0
GitHub: NA
Source code: https://github.com/cran/rbioacc
Date/Publication: 2023-09-21 09:30:06 UTC
Number of recursive dependencies: 106

Run revdepcheck::revdep_details(, "rbioacc") for more info

checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

RHMS

Version: 1.7
GitHub: NA
Source code: https://github.com/cran/RHMS
Date/Publication: 2021-09-27 15:50:02 UTC
Number of recursive dependencies: 96

Run revdepcheck::revdep_details(, "RHMS") for more info

checking whether package ‘RHMS’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘network’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/RHMS/new/RHMS.Rcheck/00install.out’ for details.

ridgetorus

Version: 1.0.2
GitHub: https://github.com/egarpor/ridgetorus
Source code: https://github.com/cran/ridgetorus
Date/Publication: 2023-08-27 22:40:02 UTC
Number of recursive dependencies: 142

Run revdepcheck::revdep_details(, "ridgetorus") for more info

checking whether package ‘ridgetorus’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘Rcpp’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/ridgetorus/new/ridgetorus.Rcheck/00install.out’ for details.

robCompositions

Version: 2.4.1
GitHub: NA
Source code: https://github.com/cran/robCompositions
Date/Publication: 2023-08-25 15:30:06 UTC
Number of recursive dependencies: 143

Run revdepcheck::revdep_details(, "robCompositions") for more info

checking whether package ‘robCompositions’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 Warning: package ‘pls’ was built under R version 4.3.1 Warning: package ‘data.table’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/robCompositions/new/robCompositions.Rcheck/00install.out’ for details.
checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

robustbase

Version: 0.99-2
GitHub: NA
Source code: https://github.com/cran/robustbase
Date/Publication: 2024-01-27 16:30:02 UTC
Number of recursive dependencies: 78

Run revdepcheck::revdep_details(, "robustbase") for more info

checking whether package ‘robustbase’ can be installed ... ERROR Installation failed. See ‘/ggally/revdep/checks.noindex/robustbase/new/robustbase.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘robustX’

* installing *source* package ‘robustbase’ ...
** package ‘robustbase’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
sh: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
using SDK: ‘MacOSX14.2.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c R-rng4ftn.c -o R-rng4ftn.o
/opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran  -fPIC  -Wall -g -O2  -c eigen.f -o eigen.o
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
...
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
/opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran  -fPIC  -Wall -g -O2  -c rfltsreg.f -o rfltsreg.o
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
make: *** [eigen.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [rfltsreg.o] Error 1
make: *** [rffastmcd.o] Error 1
make: *** [rf-common.o] Error 1
ERROR: compilation failed for package ‘robustbase’
* removing ‘/ggally/revdep/checks.noindex/robustbase/new/robustbase.Rcheck/robustbase’

* installing *source* package ‘robustbase’ ...
** package ‘robustbase’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
sh: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
using SDK: ‘MacOSX14.2.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c R-rng4ftn.c -o R-rng4ftn.o
/opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran  -fPIC  -Wall -g -O2  -c eigen.f -o eigen.o
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
...
/opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran  -fPIC  -Wall -g -O2  -c rf-common.f -o rf-common.o
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
/opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran  -fPIC  -Wall -g -O2  -c rffastmcd.f -o rffastmcd.o
make: /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran: No such file or directory
make: *** [eigen.o] Error 1
make: *** Waiting for unfinished jobs....
make: *** [rf-common.o] Error 1
make: *** [rffastmcd.o] Error 1
ERROR: compilation failed for package ‘robustbase’
* removing ‘/ggally/revdep/checks.noindex/robustbase/old/robustbase.Rcheck/robustbase’

rrr

Version: 1.0.0
GitHub: https://github.com/chrisaddy/rrr
Source code: https://github.com/cran/rrr
Date/Publication: 2016-12-09 15:15:55
Number of recursive dependencies: 104

Run revdepcheck::revdep_details(, "rrr") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.

rwty

Version: 1.0.2
GitHub: NA
Source code: https://github.com/cran/rwty
Date/Publication: 2019-02-15 15:10:03 UTC
Number of recursive dependencies: 102

Run revdepcheck::revdep_details(, "rwty") for more info

checking whether package ‘rwty’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/rwty/new/rwty.Rcheck/00install.out’ for details.

sageR

Version: 0.6.1
GitHub: https://github.com/fbertran/sageR
Source code: https://github.com/cran/sageR
Date/Publication: 2023-03-23 18:40:02 UTC
Number of recursive dependencies: 249

Run revdepcheck::revdep_details(, "sageR") for more info

checking data for non-ASCII characters ... NOTE Note: found 120 marked UTF-8 strings

scPipe

Version: 2.2.0
GitHub: https://github.com/LuyiTian/scPipe
Source code: https://github.com/cran/scPipe
Date/Publication: 2023-10-24
Number of recursive dependencies: 260

Run revdepcheck::revdep_details(, "scPipe") for more info

checking whether package ‘scPipe’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘SingleCellExperiment’ was built under R version 4.3.2 Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 Warning: package ‘MatrixGenerics’ was built under R version 4.3.1 Warning: package ‘matrixStats’ was built under R version 4.3.1 Warning: package ‘GenomicRanges’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘IRanges’ was built under R version 4.3.1 Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 Warning: package ‘Biobase’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/scPipe/new/scPipe.Rcheck/00install.out’ for details.
checking C++ specification ... NOTE Specified C++11: please drop specification unless essential
checking installed package size ... NOTE installed size is 17.0Mb sub-directories of 1Mb or more: doc 1.5Mb extdata 12.1Mb libs 2.1Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘flexmix’ ‘vctrs’ All declared Imports should be used.
checking R code for possible problems ... NOTE sc_atac_feature_counting: warning in sc_atac_create_sce(input_folder = output_folder, organism = organism, sample = sample_name, feature_type = feature_type, pheno_data = pheno_data, report = create_report): partial argument match of 'sample' to 'sample_name' sc_aligning: no visible binding for global variable ‘Var1’ sc_aligning: no visible binding for global variable ‘Freq’ sc_atac_bam_tagging: no visible binding for global variable ‘.N’ sc_atac_bam_tagging: no visible binding for global variable ‘count’ sc_atac_bam_tagging: no visible binding for global variable ‘.SD’ sc_atac_create_cell_qc_metrics: no visible binding for global variable ... sc_mae_plot_umap: no visible binding for global variable ‘UMAP2’ Undefined global functions or variables: ..count.. .N .SD Freq UMAP1 UMAP2 Var1 barcode cluster count end experiments irlba log_cells_per_feature log_counts_per_cell log_counts_per_feature log_features_per_cell seqnames start value write.csv Consider adding importFrom("stats", "end", "start") importFrom("utils", "write.csv") to your NAMESPACE file.
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

SeqSQC

Version: 1.24.0
GitHub: https://github.com/Liubuntu/SeqSQC
Source code: https://github.com/cran/SeqSQC
Date/Publication: 2023-10-24
Number of recursive dependencies: 144

Run revdepcheck::revdep_details(, "SeqSQC") for more info

checking package dependencies ... ERROR ``` Package required but not available: ‘rbokeh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

SimBIID

Version: 0.2.1
GitHub: https://github.com/tjmckinley/SimBIID
Source code: https://github.com/cran/SimBIID
Date/Publication: 2021-02-04 05:20:02 UTC
Number of recursive dependencies: 79

Run revdepcheck::revdep_details(, "SimBIID") for more info

checking C++ specification ... NOTE Specified C++11: please drop specification unless essential

simmr

Version: 0.5.1.216
GitHub: https://github.com/andrewcparnell/simmr
Source code: https://github.com/cran/simmr
Date/Publication: 2023-10-27 14:20:02 UTC
Number of recursive dependencies: 129

Run revdepcheck::revdep_details(, "simmr") for more info

checking whether package ‘simmr’ can be installed ... ERROR Installation failed. See ‘/ggally/revdep/checks.noindex/simmr/new/simmr.Rcheck/00install.out’ for details.

* installing *source* package ‘simmr’ ...
** package ‘simmr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX14.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/ggally/revdep/library.noindex/simmr/Rcpp/include' -I'/ggally/revdep/library.noindex/simmr/RcppArmadillo/include' -I'/ggally/revdep/library.noindex/simmr/RcppDist/include' -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/ggally/revdep/library.noindex/simmr/Rcpp/include' -I'/ggally/revdep/library.noindex/simmr/RcppArmadillo/include' -I'/ggally/revdep/library.noindex/simmr/RcppDist/include' -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c run_VB.cpp -o run_VB.o
run_VB.cpp:6:21: warning: unused variable 'log2pi' [-Wunused-const-variable]
static double const log2pi = std::log(2.0 * M_PI);
...
  dlopen(/ggally/revdep/library.noindex/simmr/rjags/libs/rjags.so, 0x000A): Library not loaded: /usr/local/lib/libjags.4.dylib
  Referenced from: <621A7307-C96A-3A25-BE2B-B9C2339518AE> /ggally/revdep/library.noindex/simmr/rjags/libs/rjags.so
  Reason: tried: '/usr/local/lib/libjags.4.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libjags.4.dylib' (no such file), '/usr/local/lib/libjags.4.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libjags.4.dy
In addition: Warning messages:
1: package ‘R2jags’ was built under R version 4.3.1
2: package ‘rjags’ was built under R version 4.3.1
3: package ‘coda’ was built under R version 4.3.1
Execution halted
ERROR: lazy loading failed for package ‘simmr’
* removing ‘/ggally/revdep/checks.noindex/simmr/new/simmr.Rcheck/simmr’

* installing *source* package ‘simmr’ ...
** package ‘simmr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX14.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/ggally/revdep/library.noindex/simmr/Rcpp/include' -I'/ggally/revdep/library.noindex/simmr/RcppArmadillo/include' -I'/ggally/revdep/library.noindex/simmr/RcppDist/include' -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/ggally/revdep/library.noindex/simmr/Rcpp/include' -I'/ggally/revdep/library.noindex/simmr/RcppArmadillo/include' -I'/ggally/revdep/library.noindex/simmr/RcppDist/include' -I/opt/R/arm64/include -I/usr/local/include -Xclang -fopenmp    -fPIC  -falign-functions=64 -Wall -g -O2  -c run_VB.cpp -o run_VB.o
run_VB.cpp:6:21: warning: unused variable 'log2pi' [-Wunused-const-variable]
static double const log2pi = std::log(2.0 * M_PI);
...
  dlopen(/ggally/revdep/library.noindex/simmr/rjags/libs/rjags.so, 0x000A): Library not loaded: /usr/local/lib/libjags.4.dylib
  Referenced from: <621A7307-C96A-3A25-BE2B-B9C2339518AE> /ggally/revdep/library.noindex/simmr/rjags/libs/rjags.so
  Reason: tried: '/usr/local/lib/libjags.4.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libjags.4.dylib' (no such file), '/usr/local/lib/libjags.4.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libjags.4.dy
In addition: Warning messages:
1: package ‘R2jags’ was built under R version 4.3.1
2: package ‘rjags’ was built under R version 4.3.1
3: package ‘coda’ was built under R version 4.3.1
Execution halted
ERROR: lazy loading failed for package ‘simmr’
* removing ‘/ggally/revdep/checks.noindex/simmr/old/simmr.Rcheck/simmr’

SmartEDA

Version: 0.3.10
GitHub: https://github.com/daya6489/SmartEDA
Source code: https://github.com/cran/SmartEDA
Date/Publication: 2024-01-30 17:50:02 UTC
Number of recursive dependencies: 108

Run revdepcheck::revdep_details(, "SmartEDA") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘qpdf’ All declared Imports should be used.
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘ggthemes’, ‘DataExplorer’

SPOTMisc

Version: 1.19.52
GitHub: NA
Source code: https://github.com/cran/SPOTMisc
Date/Publication: 2022-09-05 15:10:02 UTC
Number of recursive dependencies: 181

Run revdepcheck::revdep_details(, "SPOTMisc") for more info

checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: data 4.7Mb

staRdom

Version: 1.1.28
GitHub: https://github.com/MatthiasPucher/staRdom
Source code: https://github.com/cran/staRdom
Date/Publication: 2023-06-16 08:20:02 UTC
Number of recursive dependencies: 158

Run revdepcheck::revdep_details(, "staRdom") for more info

checking whether package ‘staRdom’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/staRdom/new/staRdom.Rcheck/00install.out’ for details.

statVisual

Version: 1.2.1
GitHub: NA
Source code: https://github.com/cran/statVisual
Date/Publication: 2020-02-20 19:30:02 UTC
Number of recursive dependencies: 194

Run revdepcheck::revdep_details(, "statVisual") for more info

checking whether package ‘statVisual’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘Biobase’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/statVisual/new/statVisual.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’ All declared Imports should be used.

survstan

Version: 0.0.6.1
GitHub: https://github.com/fndemarqui/survstan
Source code: https://github.com/cran/survstan
Date/Publication: 2024-02-05 15:00:02 UTC
Number of recursive dependencies: 123

Run revdepcheck::revdep_details(, "survstan") for more info

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used.
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

systemPipeTools

Version: 1.10.0
GitHub: NA
Source code: https://github.com/cran/systemPipeTools
Date/Publication: 2023-10-24
Number of recursive dependencies: 164

Run revdepcheck::revdep_details(, "systemPipeTools") for more info

checking dependencies in R code ... WARNING Missing or unexported object: ‘BiocGenerics::rowSums’

tidybulk

Version: 1.14.3
GitHub: https://github.com/stemangiola/tidybulk
Source code: https://github.com/cran/tidybulk
Date/Publication: 2023-12-04
Number of recursive dependencies: 400

Run revdepcheck::revdep_details(, "tidybulk") for more info

checking whether package ‘tidybulk’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ttservice’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/tidybulk/new/tidybulk.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: data 2.3Mb help 1.2Mb
checking R code for possible problems ... NOTE .adjust_abundance_se: no visible binding for global variable ‘x’ .aggregate_duplicates_se: no visible binding for global variable ‘group_name’ .aggregate_duplicates_se: no visible binding for global variable ‘group’ .deconvolve_cellularity_se: no visible binding for global variable ‘X_cibersort’ .describe_transcript_SE: no visible binding for global variable ‘transcript’ .describe_transcript_SE: no visible binding for global variable ... predict prop rc read count ref_genome rotated dimensions sample 1 sample 2 sample a sample b sample_idx samples sdev seurat_clusters surv_test temp term test tot tot_filt transcript transcript_upper tt_columns update.formula upper value variable vcov web_page where with_groups x Consider adding importFrom("base", "sample") importFrom("stats", "AIC", "anova", "coef", "kmeans", "logLik", "predict", "update.formula", "vcov") to your NAMESPACE file.

tidyseurat

Version: 0.8.0
GitHub: https://github.com/stemangiola/tidyseurat
Source code: https://github.com/cran/tidyseurat
Date/Publication: 2024-01-10 04:50:02 UTC
Number of recursive dependencies: 206

Run revdepcheck::revdep_details(, "tidyseurat") for more info

checking whether package ‘tidyseurat’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘ttservice’ was built under R version 4.3.1 Warning: package ‘SeuratObject’ was built under R version 4.3.1 Warning: package ‘sp’ was built under R version 4.3.1 Warning: package ‘dplyr’ was built under R version 4.3.1 Warning: package ‘tidyr’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/tidyseurat/new/tidyseurat.Rcheck/00install.out’ for details.

tidySingleCellExperiment

Version: 1.12.0
GitHub: https://github.com/stemangiola/tidySingleCellExperiment
Source code: https://github.com/cran/tidySingleCellExperiment
Date/Publication: 2023-10-24
Number of recursive dependencies: 222

Run revdepcheck::revdep_details(, "tidySingleCellExperiment") for more info

checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
1. ├─BiocSingular::runPCA(...)
2. └─BiocSingular::runPCA(...)
3. └─BiocSingular (local) .local(x, ...)
4. ├─BiocSingular::runSVD(...)
5. └─BiocSingular::runSVD(...)
6. ├─BiocSingular::runSVD(...)
7. └─BiocSingular::runSVD(...)
8. ├─base::do.call(...)
9. └─BiocSingular (local) <fn>(...)
10. ├─base::do.call(...)
11. └─irlba (local) <fn>(...)
[ FAIL 1 | WARN 7 | SKIP 0 | PASS 154 ] Error: Test failures Execution halted ```
checking whether package ‘tidySingleCellExperiment’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘SingleCellExperiment’ was built under R version 4.3.2 Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 Warning: package ‘MatrixGenerics’ was built under R version 4.3.1 Warning: package ‘matrixStats’ was built under R version 4.3.1 Warning: package ‘GenomicRanges’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘IRanges’ was built under R version 4.3.1 Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 Warning: package ‘Biobase’ was built under R version 4.3.1 Warning: package ‘dplyr’ was built under R version 4.3.1 Warning: package ‘tidyr’ was built under R version 4.3.1 Warning: package ‘ttservice’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/tidySingleCellExperiment/new/tidySingleCellExperiment.Rcheck/00install.out’ for details.
checking R code for possible problems ... NOTE aggregate_cells,SingleCellExperiment: no visible binding for global variable ‘my_id_to_split_by___’ aggregate_cells,SingleCellExperiment: no visible binding for global variable ‘assay_name’ aggregate_cells,SingleCellExperiment: no visible global function definition for ‘join_by’ aggregate_cells,SingleCellExperiment: no visible binding for global variable ‘.feature’ Undefined global functions or variables: .feature assay_name join_by my_id_to_split_by___
checking Rd files ... NOTE prepare_Rd: group_by.Rd:98-100: Dropping empty section \seealso

TNBC.CMS

Version: 1.18.0
GitHub: NA
Source code: https://github.com/cran/TNBC.CMS
Date/Publication: 2023-10-24
Number of recursive dependencies: 174

Run revdepcheck::revdep_details(, "TNBC.CMS") for more info

checking whether package ‘TNBC.CMS’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘e1071’ was built under R version 4.3.1 Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 Warning: package ‘MatrixGenerics’ was built under R version 4.3.1 Warning: package ‘matrixStats’ was built under R version 4.3.1 Warning: package ‘GenomicRanges’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘IRanges’ was built under R version 4.3.1 Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 Warning: package ‘Biobase’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/TNBC.CMS/new/TNBC.CMS.Rcheck/00install.out’ for details.

TOAST

Version: 1.16.0
GitHub: https://github.com/ziyili20/TOAST
Source code: https://github.com/cran/TOAST
Date/Publication: 2023-10-24
Number of recursive dependencies: 118

Run revdepcheck::revdep_details(, "TOAST") for more info

checking whether package ‘TOAST’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘EpiDISH’ was built under R version 4.3.1 Warning: package ‘limma’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/TOAST/new/TOAST.Rcheck/00install.out’ for details.

TOmicsVis

Version: 2.0.0
GitHub: https://github.com/benben-miao/TOmicsVis
Source code: https://github.com/cran/TOmicsVis
Date/Publication: 2023-08-28 18:30:02 UTC
Number of recursive dependencies: 265

Run revdepcheck::revdep_details(, "TOmicsVis") for more info

checking whether package ‘TOmicsVis’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘widgetTools’ was built under R version 4.3.1 Warning: package ‘DynDoc’ was built under R version 4.3.1 Warning: package ‘Biobase’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘e1071’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/TOmicsVis/new/TOmicsVis.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: data-tables 1.4Mb doc 1.9Mb help 1.2Mb

TVTB

Version: 1.28.0
GitHub: https://github.com/kevinrue/TVTB
Source code: https://github.com/cran/TVTB
Date/Publication: 2023-11-02
Number of recursive dependencies: 192

Run revdepcheck::revdep_details(, "TVTB") for more info

checking Rd files ... WARNING checkRd: (5) VcfBasicRules-class.Rd:133-136: \item in \describe must have non-empty label checkRd: (5) VcfBasicRules-class.Rd:137-140: \item in \describe must have non-empty label checkRd: (5) VcfBasicRules-class.Rd:141-146: \item in \describe must have non-empty label checkRd: (5) VcfBasicRules-class.Rd:147-151: \item in \describe must have non-empty label checkRd: (5) VcfBasicRules-class.Rd:161-164: \item in \describe must have non-empty label checkRd: (5) VcfBasicRules-class.Rd:165-168: \item in \describe must have non-empty label checkRd: (5) VcfBasicRules-class.Rd:179-192: \item in \describe must have non-empty label checkRd: (5) VcfBasicRules-class.Rd:193-201: \item in \describe must have non-empty label checkRd: (5) VcfFilterRules-class.Rd:85-92: \item in \describe must have non-empty label checkRd: (5) VcfFilterRules-class.Rd:93-96: \item in \describe must have non-empty label checkRd: (5) VcfFilterRules-class.Rd:97-103: \item in \describe must have non-empty label checkRd: (5) VcfFilterRules-class.Rd:104-108: \item in \describe must have non-empty label checkRd: (5) VcfFilterRules-class.Rd:120-123: \item in \describe must have non-empty label checkRd: (5) VcfFilterRules-class.Rd:124-127: \item in \describe must have non-empty label checkRd: (5) VcfFilterRules-class.Rd:134-140: \item in \describe must have non-empty label checkRd: (5) VcfFilterRules-class.Rd:141-149: \item in \describe must have non-empty label
checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: R 2.1Mb doc 2.8Mb

ubiquity

Version: 2.0.1
GitHub: https://github.com/john-harrold/ubiquity
Source code: https://github.com/cran/ubiquity
Date/Publication: 2023-10-29 20:50:02 UTC
Number of recursive dependencies: 146

Run revdepcheck::revdep_details(, "ubiquity") for more info

checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: doc 6.6Mb ubinc 2.0Mb

ushr

Version: 0.2.3
GitHub: https://github.com/SineadMorris/ushr
Source code: https://github.com/cran/ushr
Date/Publication: 2020-04-21 18:20:03 UTC
Number of recursive dependencies: 92

Run revdepcheck::revdep_details(, "ushr") for more info

checking whether package ‘ushr’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘dplyr’ was built under R version 4.3.1 Warning: package ‘tidyr’ was built under R version 4.3.1 Warning: package ‘ggplot2’ was built under R version 4.3.1 See ‘/ggally/revdep/checks.noindex/ushr/new/ushr.Rcheck/00install.out’ for details.

velociraptor

Version: 1.12.0
GitHub: https://github.com/kevinrue/velociraptor
Source code: https://github.com/cran/velociraptor
Date/Publication: 2023-10-24
Number of recursive dependencies: 237

Run revdepcheck::revdep_details(, "velociraptor") for more info

checking examples ... ERROR ``` Running examples in ‘velociraptor-Ex.R’ failed The error most likely occurred in:

Name: embedVelocity

Title: Project velocities onto an embedding

Aliases: embedVelocity embedVelocity,ANY-method

embedVelocity,SingleCellExperiment-method

** Examples

... To search for alternate channels that may provide the conda package you're looking for, navigate to
```
https://anaconda.org
```
and use the search bar at the top of the page.

Error: one or more Python packages failed to install [error code 1] Execution halted ```
checking tests ... ``` Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Backtrace: ▆
1. ├─velociraptor::scvelo(...) at test-scvelo.R:70:5
2. └─velociraptor::scvelo(...)
3. └─velociraptor (local) .local(x, ...)
4. └─basilisk::basiliskRun(...)
5. └─basilisk::basiliskStart(...)
6. └─basilisk::obtainEnvironmentPath(env)
7. └─basilisk::setupBasiliskEnv(...)
8. └─reticulate::conda_install(...)
9. └─reticulate:::stopf(fmt, result)
[ FAIL 6 | WARN 14 | SKIP 0 | PASS 0 ] Error: Test failures Execution halted ```
checking whether package ‘velociraptor’ can be installed ... WARNING Found the following significant warnings: Warning: package ‘SummarizedExperiment’ was built under R version 4.3.2 Warning: package ‘MatrixGenerics’ was built under R version 4.3.1 Warning: package ‘matrixStats’ was built under R version 4.3.1 Warning: package ‘GenomicRanges’ was built under R version 4.3.1 Warning: package ‘BiocGenerics’ was built under R version 4.3.1 Warning: package ‘S4Vectors’ was built under R version 4.3.2 Warning: package ‘IRanges’ was built under R version 4.3.1 Warning: package ‘GenomeInfoDb’ was built under R version 4.3.2 Warning: package ‘Biobase’ was built under R version 4.3.1 Found the following additional notes/warnings: Non-staged installation was used See ‘/ggally/revdep/checks.noindex/velociraptor/new/velociraptor.Rcheck/00install.out’ for details.

vidger

Version: 1.22.0
GitHub: https://github.com/btmonier/vidger
Source code: https://github.com/cran/vidger
Date/Publication: 2023-10-24
Number of recursive dependencies: 128

Run revdepcheck::revdep_details(, "vidger") for more info

checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: data 3.0Mb doc 6.2Mb

WOTPLY

Version: 0.1.0
GitHub: NA
Source code: https://github.com/cran/WOTPLY
Date/Publication: 2022-09-12 07:43:01 UTC
Number of recursive dependencies: 83

Run revdepcheck::revdep_details(, "WOTPLY") for more info

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘sna’ All declared Imports should be used.

ggobi/ggally documentation built on May 9, 2024, 7:21 a.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

ggobi/ggally Extension to 'ggplot2'

revdep/problems.md In ggobi/ggally: Extension to 'ggplot2'

adventr

In both

airGR

In both

Installation

Devel

CRAN

alevinQC

In both

AlpsNMR

In both

AntMAN

In both

BasketballAnalyzeR

In both

BindingSiteFinder

In both

bootcluster

In both

CARBayes

In both

CARBayesST

In both

CeTF

In both

CINNA

In both

CluMSID

In both

clustrd

In both

communication

In both

conserveR

In both

corrViz

In both

coveffectsplot

In both

covsim

In both

cyanoFilter

In both

descriptio

In both

fect

In both

fic

In both

finalfit

In both

fingerPro

In both

Installation

Devel

CRAN

FPDclustering

In both

fpp2

In both

freqparcoord

In both

gatom

In both

GENESIS

In both

GeomxTools

In both

gfilmm

In both

ggbio

In both

Name: autoplot

Title: Generic autoplot function

Aliases: autoplot autoplot,GRanges-method autoplot,GRangesList-method

autoplot,IRanges-method autoplot,Seqinfo-method

autoplot,BSgenome-method autoplot,GAlignments-method

autoplot,BamFile-method autoplot,BamFileList-method

ggobi/ggally
Extension to 'ggplot2'

revdep/problems.md
In ggobi/ggally: Extension to 'ggplot2'