CRAN Package Check Results for Package SourceSet

Last updated on 2019-10-13 10:47:09 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.1	3.89	38.07	41.96	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.1	2.86	29.94	32.80	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.1			49.91	ERROR
r-devel-linux-x86_64-fedora-gcc	0.1.1			51.98	ERROR
r-devel-windows-ix86+x86_64	0.1.1	8.00	47.00	55.00	ERROR
r-patched-linux-x86_64	0.1.1	3.70	36.53	40.23	ERROR
r-patched-solaris-x86	0.1.1			73.90	ERROR
r-release-linux-x86_64	0.1.1	3.34	36.64	39.98	ERROR
r-release-windows-ix86+x86_64	0.1.1	12.00	58.00	70.00	ERROR
r-release-osx-x86_64	0.1.1				WARN
r-oldrel-windows-ix86+x86_64	0.1.1	5.00	115.00	120.00	NOTE
r-oldrel-osx-x86_64	0.1.1				WARN

Check Details

Version: 0.1.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'r2cytoscape'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.1.1
Check: dependencies in R code
Result: NOTE
Missing or unexported object: 'gRbase::is.TUG.graphNEL'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64

Version: 0.1.1
Check: examples
Result: ERROR
    Running examples in 'SourceSet-Ex.R' failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: ripAllRootsClique
    > ### Title: All possible RIP orderings
    > ### Aliases: ripAllRootsClique
    >
    > ### ** Examples
    >
    > if(require(gRbase)){
    +
    + ## decomposable graph
    + ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
    + ug.rip.all<-ripAllRootsClique(ug.graph)
    + # 7 variables
    + length(ug.rip.all$elements$variables)
    + # 3 max.cliques
    + length(ug.rip.all$elements$cliques)
    + # 7 unique components
    + nrow(ug.rip.all$elements$components)
    + # all rip orderings:
    + ug.rip.all$indices$ordering
    +
    + ## directed graph
    + dag.graph<-dag(~3:1+3:2+4:3)
    + dag.rip.all<-ripAllRootsClique(dag.graph)
    + # triangulated and morliazed graph
    + dag.rip.all$graph
    + # all rip orderings
    + dag.rip.all$indices$ordering
    + }
    Loading required package: gRbase
    Error: 'is.TUG.graphNEL' is not an exported object from 'namespace:gRbase'
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'SourceSet.Rmd' using rmarkdown
    Loading required package: graph
    Loading required package: BiocGenerics
    Loading required package: parallel

    Attaching package: 'BiocGenerics'

    The following objects are masked from 'package:parallel':

     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB

    The following objects are masked from 'package:stats':

     IQR, mad, sd, var, xtabs

    The following objects are masked from 'package:base':

     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect,
     is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
     pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
     setdiff, sort, table, tapply, union, unique, unsplit, which,
     which.max, which.min

    Identifing all possible orderings..
    Quitting from lines 164-166 (SourceSet.Rmd)
    Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
    'is.TUG.graphNEL' is not an exported object from 'namespace:gRbase'
    --- failed re-building 'SourceSet.Rmd'

    SUMMARY: processing the following file failed:
     'SourceSet.Rmd'

    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.1.1
Check: examples
Result: ERROR
    Running examples in ‘SourceSet-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: ripAllRootsClique
    > ### Title: All possible RIP orderings
    > ### Aliases: ripAllRootsClique
    >
    > ### ** Examples
    >
    > if(require(gRbase)){
    +
    + ## decomposable graph
    + ug.graph<-ug(~1:2:3+3:4+4:5:6:7)
    + ug.rip.all<-ripAllRootsClique(ug.graph)
    + # 7 variables
    + length(ug.rip.all$elements$variables)
    + # 3 max.cliques
    + length(ug.rip.all$elements$cliques)
    + # 7 unique components
    + nrow(ug.rip.all$elements$components)
    + # all rip orderings:
    + ug.rip.all$indices$ordering
    +
    + ## directed graph
    + dag.graph<-dag(~3:1+3:2+4:3)
    + dag.rip.all<-ripAllRootsClique(dag.graph)
    + # triangulated and morliazed graph
    + dag.rip.all$graph
    + # all rip orderings
    + dag.rip.all$indices$ordering
    + }
    Loading required package: gRbase
    Error: 'is.TUG.graphNEL' is not an exported object from 'namespace:gRbase'
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘SourceSet.Rmd’ using rmarkdown
    Loading required package: graph
    Loading required package: BiocGenerics
    Loading required package: parallel

    Attaching package: 'BiocGenerics'

    The following objects are masked from 'package:parallel':

     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB

    The following objects are masked from 'package:stats':

     IQR, mad, sd, var, xtabs

    The following objects are masked from 'package:base':

     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect,
     is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
     pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
     setdiff, sort, table, tapply, union, unique, unsplit, which,
     which.max, which.min

    Identifing all possible orderings..
    Quitting from lines 164-166 (SourceSet.Rmd)
    Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
    'is.TUG.graphNEL' is not an exported object from 'namespace:gRbase'
    --- failed re-building ‘SourceSet.Rmd’

    SUMMARY: processing the following file failed:
     ‘SourceSet.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘SourceSet.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Loading required package: graph
    Loading required package: BiocGenerics
    Loading required package: parallel

    Attaching package: 'BiocGenerics'

    The following objects are masked from 'package:parallel':

     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB

    The following objects are masked from 'package:stats':

     IQR, mad, sd, var, xtabs

    The following objects are masked from 'package:base':

     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect,
     is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
     pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
     setdiff, sort, table, tapply, union, unique, unsplit, which,
     which.max, which.min

    Identifing all possible orderings..
    Quitting from lines 164-166 (SourceSet.Rmd)
    Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
    'is.TUG.graphNEL' is not an exported object from 'namespace:gRbase'
    --- failed re-building ‘SourceSet.Rmd’

    SUMMARY: processing the following file failed:
     ‘SourceSet.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.1.1
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'r2cytoscape', 'BiocStyle', 'hgu95av2.db', 'ALL', 'org.Hs.eg.db'
Flavor: r-release-osx-x86_64

Version: 0.1.1
Check: Rd cross-references
Result: NOTE
Packages unavailable to check Rd xrefs: ‘ALL’, ‘simPATHy’
Flavor: r-release-osx-x86_64

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘SourceSet.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Loading required package: graph
    Loading required package: BiocGenerics
    Loading required package: parallel

    Attaching package: 'BiocGenerics'

    The following objects are masked from 'package:parallel':

     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB

    The following objects are masked from 'package:stats':

     IQR, mad, sd, var, xtabs

    The following objects are masked from 'package:base':

     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect,
     is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
     pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
     setdiff, sort, table, tapply, union, unique, unsplit, which,
     which.max, which.min

    Identifing all possible orderings..
    Total run time: 1.42 secs
    Identifing all possible orderings..
    Total run time: 0.79 secs
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Warning in normalizePath(f2) :
     path[1]="webshotb0c21dfb4fd0.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file 'webshotb0c21dfb4fd0.png': No such file or directory
    Quitting from lines 346-347 (SourceSet.Rmd)
    Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘SourceSet.Rmd’

    SUMMARY: processing the following file failed:
     ‘SourceSet.Rmd’

    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.1.1
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’
Flavor: r-oldrel-osx-x86_64

Version: 0.1.1
Check: Rd cross-references
Result: NOTE
Packages unavailable to check Rd xrefs: ‘simPATHy’, ‘graphite’
Flavor: r-oldrel-osx-x86_64

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
     IQR, mad, sd, var, xtabs

    The following objects are masked from 'package:base':

     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colMeans, colSums, colnames,
     dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
     intersect, is.unsorted, lapply, lengths, mapply, match, mget,
     order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
     rowMeans, rowSums, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min

    Identifing all possible orderings..
    Total run time: 1.21 secs
    Identifing all possible orderings..
    Total run time: 0.86 secs
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Warning in normalizePath(f2) :
     path[1]="./webshotf9064431846f.png": No such file or directory
    Warning in file(con, "rb") :
     cannot open file './webshotf9064431846f.png': No such file or directory
    Quitting from lines 346-347 (SourceSet.Rmd)
    Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-oldrel-osx-x86_64