CRAN Package Check Results for Package HDMD

Last updated on 2017-02-24 23:52:30.

Flavor	Version	T_install	T_check	T_total	Status	Flags
r-devel-linux-x86_64-debian-clang	1.2	0.76	19.82	20.58	NOTE
r-devel-linux-x86_64-debian-gcc	1.2	0.80	19.69	20.49	NOTE
r-devel-linux-x86_64-fedora-clang	1.2			36.60	NOTE	--no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc	1.2			35.47	NOTE	--no-stop-on-test-error
r-devel-macos-x86_64-clang	1.2			30.93	NOTE	--no-stop-on-test-error
r-devel-windows-ix86+x86_64	1.2	8.00	40.00	48.00	NOTE
r-patched-linux-x86_64	1.2	0.75	16.78	17.53	NOTE
r-patched-solaris-sparc	1.2			198.00	NOTE
r-patched-solaris-x86	1.2			40.50	NOTE
r-release-linux-x86_64	1.2	0.67	16.87	17.53	NOTE
r-release-osx-x86_64-mavericks	1.2				NOTE
r-release-windows-ix86+x86_64	1.2	5.00	49.00	54.00	NOTE
r-oldrel-windows-ix86+x86_64	1.2	8.00	78.00	86.00	OK

Check Details

Version: 1.2
Check: R code for possible problems
Result: NOTE
    Promax.only: no visible global function definition for ‘lm.fit’
    factor.pa.ginv: no visible binding for global variable ‘median’
    factor.pa.ginv: no visible global function definition for ‘cor’
    factor.pa.ginv: no visible global function definition for ‘varimax’
    factor.pa.ginv: no visible global function definition for ‘pchisq’
    pairwise.mahalanobis: no visible global function definition for ‘cor’
    pairwise.mahalanobis: no visible global function definition for
     ‘mahalanobis’
    Undefined global functions or variables:
     cor lm.fit mahalanobis median pchisq varimax
    Consider adding
     importFrom("stats", "cor", "lm.fit", "mahalanobis", "median", "pchisq",
     "varimax")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.2
Check: Rd line widths
Result: NOTE
    Rd file 'AminoAcids.Rd':
     \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
     legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

    Rd file 'FactorTransform.Rd':
     \usage lines wider than 90 characters:
     FactorTransform(Source, Search = AminoAcids, Replace = AAMetric.Atchley, Factor = 1, bycol = TRUE, SeqName = NULL, alignment=FALSE, fi ... [TRUNCATED]

    Rd file 'HDMD-package.Rd':
     \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     plot(-1*AA54_lda_RawMetric1Centered[,1], -1*AA54_lda_RawMetric1Centered[,2], pch = grouping, xlab="Canonical Variate 1", ylab="Canonica ... [TRUNCATED]

    Rd file 'NMI.Rd':
     \usage lines wider than 90 characters:
     NMI(Hx, Hy, Hxy, type = c("NULL", "marginal", "joint", "min.marginal", "max.marginal", "min.conditional", "max.conditional"))

    Rd file 'factor.pa.ginv.Rd':
     \usage lines wider than 90 characters:
     factor.pa.ginv(r, nfactors = 1, residuals = FALSE, prerotate = FALSE, rotate = "varimax", m = 4, n.obs = NA, scores = c("none", "regres ... [TRUNCATED]
     \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
     legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

    These lines will be truncated in the PDF manual.
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: 1.2
Flags: --no-stop-on-test-error
Check: R code for possible problems
Result: NOTE
    Promax.only: no visible global function definition for ‘lm.fit’
    factor.pa.ginv: no visible binding for global variable ‘median’
    factor.pa.ginv: no visible global function definition for ‘cor’
    factor.pa.ginv: no visible global function definition for ‘varimax’
    factor.pa.ginv: no visible global function definition for ‘pchisq’
    pairwise.mahalanobis: no visible global function definition for ‘cor’
    pairwise.mahalanobis: no visible global function definition for
     ‘mahalanobis’
    Undefined global functions or variables:
     cor lm.fit mahalanobis median pchisq varimax
    Consider adding
     importFrom("stats", "cor", "lm.fit", "mahalanobis", "median", "pchisq",
     "varimax")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 1.2
Flags: --no-stop-on-test-error
Check: Rd line widths
Result: NOTE
    Rd file 'AminoAcids.Rd':
     \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
     legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

    Rd file 'FactorTransform.Rd':
     \usage lines wider than 90 characters:
     FactorTransform(Source, Search = AminoAcids, Replace = AAMetric.Atchley, Factor = 1, bycol = TRUE, SeqName = NULL, alignment=FALSE, fi ... [TRUNCATED]

    Rd file 'HDMD-package.Rd':
     \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     plot(-1*AA54_lda_RawMetric1Centered[,1], -1*AA54_lda_RawMetric1Centered[,2], pch = grouping, xlab="Canonical Variate 1", ylab="Canonica ... [TRUNCATED]

    Rd file 'NMI.Rd':
     \usage lines wider than 90 characters:
     NMI(Hx, Hy, Hxy, type = c("NULL", "marginal", "joint", "min.marginal", "max.marginal", "min.conditional", "max.conditional"))

    Rd file 'factor.pa.ginv.Rd':
     \usage lines wider than 90 characters:
     factor.pa.ginv(r, nfactors = 1, residuals = FALSE, prerotate = FALSE, rotate = "varimax", m = 4, n.obs = NA, scores = c("none", "regres ... [TRUNCATED]
     \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
     legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc