Last updated on 2025-05-09 01:50:39 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| AquaEnv | 13 | ||
| diagram | 2 | 11 | |
| ecolMod | 2 | 11 | |
| FME | 6 | 7 | |
| LIM | 1 | 2 | 10 |
| limSolve | 1 | 12 | |
| marelac | 13 | ||
| NetIndices | 2 | 11 | |
| OceanView | 6 | 7 | |
| plot3D | 6 | 7 | |
| plot3Drgl | 6 | 7 | |
| ReacTran | 13 | ||
| rootSolve | 13 | ||
| shape | 2 | 11 |
Current CRAN status: NOTE: 13
Version: 1.0-4
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <Karline.Soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("Andreas", "F."),
family = "Hofmann",
role = "aut"),
person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl"),
person(given = c("Filip", "J.R."),
family = "Meysman",
role = "aut"),
person(given = "Mathilde",
family = "Hagens",
role = "aut"))
as necessary.
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0-4
Check: Rd files
Result: NOTE
checkRd: (-1) BufferFactors.Rd:33: Escaped LaTeX specials: \_
checkRd: (-1) BufferFactors.Rd:34: Escaped LaTeX specials: \_
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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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 2, OK: 11
Version: 1.6.5
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: NOTE: 2, OK: 11
Version: 1.2.6.4
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl"),
person(given = c("Peter", "MJ"),
family = "Herman",
role = "aut",
email = "peter.herman@nioz.nl"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: NOTE: 6, OK: 7
Version: 1.3.6.3
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
obsplot.Rd: print.deSolve, ode, deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Current CRAN status: ERROR: 1, NOTE: 2, OK: 10
Version: 1.4.7.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl"),
person(given = "Dick",
family = "van Oevelen",
role = "aut",
email = "dick.vanoevelen@nioz.nl"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.4.7.1
Check: examples
Result: ERROR
Running examples in ‘LIM-Ex.R’ failed
The error most likely occurred in:
> ### Name: LIMEcoli
> ### Title: The Escherichia Coli Core Metabolism: Reaction network model
> ### specificiation
> ### Aliases: LIMEcoli
> ### Keywords: datasets
>
> ### ** Examples
>
>
>
> # 1. parsimonious (simplest) solution
> pars <- Ldei(LIMEcoli)
>
> # 2. the ranges of each reaction
> xr <- Xranges(LIMEcoli, central = TRUE, full = TRUE)
Warning in lsei(E = E, F = F, G = G, H = H) :
LSEI error: inequalities contradictory
[1] "problem infeasible"
Warning in xranges(lim$A, lim$B, lim$G, lim$H, ...) :
cannot proceed: problem not solvable at requested tolerance 1e-08
>
> # 3. the optimal solution - solved with linear programming
> LP <- Linp(LIMEcoli)
> Optimal <- t(LP$X)
>
> # show the results
> data.frame(pars = pars$X, Optimal, xr[ ,1:3])
Error in xr[, 1:3] : subscript out of bounds
Calls: data.frame
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.4.7.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘LIM.Rnw’ using Sweave
--- finished re-building ‘LIM.Rnw’
--- re-building ‘LIMecoli.Rnw’ using Sweave
Loading required package: limSolve
Loading required package: diagram
Loading required package: shape
Warning in lsei(E = E, F = F, G = G, H = H) :
LSEI error: inequalities contradictory
Warning in xranges(lim$A, lim$B, lim$G, lim$H, ...) :
cannot proceed: problem not solvable at requested tolerance 1e-08
Error: processing vignette 'LIMecoli.Rnw' failed with diagnostics:
chunk 7 (label = range)
Error in plot.window(xlim = xlim, ylim = ylim, log = log) :
NAs not allowed in 'xlim'
--- failed re-building ‘LIMecoli.Rnw’
SUMMARY: processing the following file failed:
‘LIMecoli.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 1.5.7.1
Check: examples
Result: ERROR
Running examples in ‘limSolve-Ex.R’ failed
The error most likely occurred in:
> ### Name: E_coli
> ### Title: An underdetermined linear inverse problem: the Escherichia Coli
> ### Core Metabolism Model.
> ### Aliases: E_coli
> ### Keywords: datasets
>
> ### ** Examples
>
> # 1. parsimonious (simplest) solution
> pars <- lsei(E = E_coli$A, F = E_coli$B, G = E_coli$G, H = E_coli$H)$X
Warning in lsei(E = E_coli$A, F = E_coli$B, G = E_coli$G, H = E_coli$H) :
LSEI error: inequalities contradictory
>
> # 2. the optimal solution - solved with linear programming
> # some unknowns can be negative
>
> LP <- linp(E = E_coli$A, F = E_coli$B,G = E_coli$G, H = E_coli$H,
+ Cost = -E_coli$Maximise, ispos = FALSE)
> (Optimal <- LP$X)
GLK1 PGI1 PFKA FBP FBA TPIA
0.000000 807.532745 781.590686 0.000000 781.590686 781.590686
GAPA PGK GPMA ENO PPSA PYKA
1541.434199 1541.434199 1492.089090 1492.089090 0.000000 466.657964
ACEE ZWF PGL GND RPIA RPE
1149.295284 0.000000 0.000000 0.000000 23.623833 -23.623833
TKTA1 TKTA2 TALA GLTA ACNA ICDA
-5.850762 -17.773070 -5.850762 35.435749 35.435749 35.435749
SUCA SUCC1 SDHA1 FRDA FUMA MDH
0.000000 0.000000 0.000000 100.000000 -100.000000 -100.000000
DLD1 ADHE2 PFLA PTA ACKA ACS
0.000000 1000.000000 10.000000 0.000000 0.000000 0.000000
PCKA PPC MAEB SFCA ACEA ACEB
0.000000 194.384939 0.000000 0.000000 0.000000 0.000000
PPA GLPK GPSA1 RBSK NUOA FDOH
0.000000 0.000000 0.000000 0.000000 140.000000 0.000000
GLPD CYOA SDHA2 PNT1A PNT2A ATPA
0.000000 40.000000 -100.000000 0.000000 567.965512 -145.466329
GLCUP GLCPTS GLUP RIBUP ACUP LACUP
0.000000 814.156250 0.000000 0.000000 0.000000 0.000000
FORUP ETHUP SUCCUP PYRUP PIUP O2TX
-10.000000 -1000.000000 -100.000000 -27.796342 120.547782 20.000000
CO2TX ATPM ADK Growth
-990.346093 5.870000 0.000000 33.117523
>
> # 3.ranges of all unknowns, including the central value and all solutions
> xr <- xranges(E = E_coli$A, F = E_coli$B, G = E_coli$G, H = E_coli$H,
+ central = TRUE, full = TRUE)
Warning in lsei(E = E, F = F, G = G, H = H) :
LSEI error: inequalities contradictory
[1] "problem infeasible"
Warning in xranges(E = E_coli$A, F = E_coli$B, G = E_coli$G, H = E_coli$H, :
cannot proceed: problem not solvable at requested tolerance 1e-08
>
> # the central point is a valid solution:
> X <- xr[ ,"central"]
Error in xr[, "central"] : subscript out of bounds
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 1.4.4.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl"),
person(given = c("Julius", "Kipyegon"),
family = "Kones",
role = "aut",
email = "jkones@uonbi.ac.ke"),
person(given = "Dick",
family = "van Oevelen",
role = "aut",
email = "dick.vanoevelen@nioz.nl"))
as necessary.
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: NOTE: 6, OK: 7
Version: 1.0.7
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.7
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
Chesapeake.Rd: Oxsat
Sylt.Rd: image2D, ImageOcean, scatter2D, Oxsat
TempTraject.Rd: image2D, ImageOcean, scatter2D, Oxsat
WSnioz.Rd: image2D, ImageOcean, scatter2D, Oxsat
moviepersp.Rd: persp3Drgl, jet.col
movieslice.Rd: slice3Drgl, jet.col, slice3D
quiver.Rd: jet.col, colkey, contour2D, image2D, arrows2D, arrows3D,
Arrows
tracers2D.Rd: colkey, contour2D, image2D, scatter2D
tracers3D.Rd: points3Drgl, colkey, scatter3D
vectorplot.Rd: jet.col, colkey, Arrows
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Current CRAN status: NOTE: 6, OK: 7
Version: 1.4.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.4.1
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
slice3D.Rd: computeContour3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Current CRAN status: NOTE: 6, OK: 7
Version: 1.0.4
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.4
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
cutrgl.Rd: par3d, open3d, material3d, plotdev
imagergl.Rd: contour2D, colkey, persp3D, perspbox, image3D,
contour3D, scatter3D, arrows3D, segments3D, text3D, image2D,
scatter2D, segments2D, text2D, arrows2D
persp3Drgl.Rd: persp3D, ribbon3D, hist3D, scatter3D, points3D,
lines3D, segments3D, slice3D, slicecont3D, isosurf3D, voxel3D,
surf3D, spheresurf3D, box3D, border3D, rect3D, perspbox, plotdev
plotrgl.Rd: material3d, par3d, open3d, arrows3D, scatter3D, plotdev,
persp3D, slice3D, surf3D
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 1.4.6.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Karline Soetaert <karline.soetaert@nioz.nl>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Karline",
family = "Soetaert",
role = c("aut", "cre"),
email = "karline.soetaert@nioz.nl")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc